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Serotonin (5-HT) is a phylogenetically conserved monoamine neurotransmitter modulating important processes in the brain. To directly visualize the release of 5-HT, we developed a genetically encoded G-protein-coupled receptor (GPCR)-activation-based 5-HT (GRAB5-HT) sensor with high sensitivity, high selectivity, subsecond kinetics and subcellular resolution. GRAB5-HT detects 5-HT release in multiple physiological and pathological conditions in both flies and mice and provides new insights into the dynamics and mechanisms of 5-HT signaling.

Aim: Fragment crystallizable (Fc) glycans modulate Fc conformations and functions, and glycan may also regulate antigen recognition. In the antibody drug development, glycosylation patterns affect antibody drug characteristics and quality control. In order to provide a global feature of N-glycan interactions in response to antigen and Fc receptor bindings, the interactions among Fc N-glycans and N-glycans’ interaction with Fc CH2 and CH3 domains have been studied. Methods: Molecular dynamics simulations were used to generate conformation ensembles of free antibody, antibody-antigen complex, antibody-human Fc-gamma-receptor-I (hFcγRI) and antibody-antigen-hFcγRI, the hydrogen bonds and radial distance distribution involving N-glycans carbohydrate chains have been analyzed. Results: Two important interaction patterns have been observed. The first is the strong but non-specific interactions between two carbohydrate chains in free antibody. Secondly, it has been found that N-glycans carbohydrate chains can directly interact with CH3 domain in free antibody, and that the distance distribution between carbohydrate chains and CH3 domain clearly differentiate the free antibody, antibody-antigen complex, antibody-hFcγRI complex, and final antibody-antigen-hFcγRI complex. Conclusions: N-glycans partially acts as allosteric sensor and respond to antigen and hFcγRI binding.

The swelling of a Nafion polymer membrane in water poured into a cell with a characteristic size close to the membrane thickness has been studied experimentally using Fourier IR spectroscopy. The interest in these studies is due to the fact that the Nafion swelling in a cell whose size greatly exceeds the membrane thickness is accompanied by intense unwinding of polymer fibers into the water bulk. However, this process had not been studied in the case where the region that can be occupied by unwound polymer fibers is limited by the cell size. It is shown that the temporal dynamics of the polymer transition from hydrophobic to hydrophilic state has some peculiar features in this case, which are determined by the cell size, isotopic composition, and preliminary treatment (intense shaking) of the liquid in which a Nafion sample swells.

Using an improved travelling wave model, we have numerically investigated the dynamics of a Q-switched bismuth-doped fibre laser. Comparison of simulation results with previously reported experimental data demonstrates good agreement of the multipeak lasing structure and the shape of the strongest pulses at various levels of pumping. We have assessed the effect of the main laser parameters on output laser characteristics and quantitatively evaluated the effects of the nonsaturable loss in the active fibre and amplified spontaneous emission on output power saturation. Based on analysis of time-dependent light intensity and gain distributions in the gain medium at different instants in time, we have formulated recommendations how to improve output laser characteristics.

Chromosomes have their own territories and dynamically translocate in response to internal and external cues. However, whether and how territories and the relocation of chromosomes are controlled by other intracellular organelles remains unknown. Upon nutrient starvation and target of rapamycin complex 1 (TORC1) inactivation, micronucleophagy, which preferentially degrades nucleolar proteins, occurs at the nucleus-vacuole junction (NVJ) in budding yeast. Ribosomal DNA (rDNA) is condensed and relocated against the NVJ, whereas nucleolar proteins move towards the NVJ for micronucleophagic degradation, causing dissociation of nucleolar proteins from rDNA. These findings imply that the NVJ is the critical platform in the directional movements of rDNA and nucleolar proteins. Here, we show that cells lacking the NVJ (NVJΔ cells) largely lost rDNA condensation and rDNA-nucleolar protein separation after TORC1 inactivation. The macronucleophagy receptor Atg39, an outer nuclear membrane protein, accumulated at the NVJ and was degraded by micronucleophagy. These suggested that macronucleophagy is also dependent on the presence of the NVJ. However, micronucleophagy, but not macronucleophagy, was abolished in NVJΔ cells. This study clearly demonstrated that vacuoles controls intranuclear events, nucleolar dynamics, from outside of the nucleus via the NVJ under the control of TORC1.

A wide range of topics was raised by the four invited speakers who took part in the session on protein structure, dynamics, and function during the 20th IUPAB Congress. Most of the emphasis was placed on understanding the underlying biological phenomena of interest although applications in drug development were also mentioned. For both these purposes, it was clear that a complete description of the dynamics of the system was as important as the structures themselves. The subjects covered included antibiotic peptides, sodium channels, the synthesis of the bacterial cell wall, and protein dynamics using X-FELs.

Dynamics of melts and solutions of high molecular weight polymers and biopolymers is controlled by topological constraints (entanglements) imposing a sliding chain motion along an effective confining tube. For linear chains, the tube size is determined by universal packing number

How tethered probes report dynamics of host polymers near the glass transition was investigated by changing the length of the flexible linkers and the number of tethering points via imaging rotational fluorescence correlation microscopy and compared with free probes of different sizes. The results show that tethering did not alter the temperature-dependence of polymer dynamics and the shape of the correlation decay reported by the probe; however, the rotation slowed down up to ≈1 decade when both ends of the probe were restricted with short alkyl chain linkers. Upon comparison with the bigger free probe, the mechanism of the slowdown was attributed to the restricted motion upon tethering for tethered probes compared to averaging over different regions of the dynamic heterogeneity for the bigger probe. If the size of the probe was comparable to that of the dynamic heterogeneity of the system, tethered probes accurately report dynamics relevant to glass transition, regardless of tethering conditions.

The relaxation dynamics of polyisoprene (PI) and nitrile butadiene rubber (NBR) chains at the SiO2 interface were directly probed as a function of distance from the SiO2 surface using time-resolved...

We report a fundamentally new nonlinear dynamic system that couples optical autocatalytic behavior to phase evolution in photoreactive binary polymer blends. Upon exposure to light, the blend undergoes spontaneous patterning into a dense arrangement of microscale polymer filaments. The filaments’ growth in turn induces local spinodal decomposition of the blend along their length, thereby regulating the spatially dynamics of phase separation. This leads to the spontaneous organization of a large-scale binary phase morphology dictated by the filament arrangement. This is a new mechanism for polymer blend organization, which couples nonlinear optical dynamics to chemical phase separation dynamics, and offers a new approach to light-directed patterning and organization of polymer and hybrid blends.

We present molecular dynamics simulations of bead-and-spring polymer chains on chemically heterogeneous, energetically disordered surfaces at near-monolayer coverages. The surfaces consist of random mixtures of weakly (W) and strongly (S) attractive sites. We explore systematically the effect of surface composition on the diffusive dynamics of the chains. The polymer diffusion coefficients have a near-Arrhenius temperature dependence, with activation energies which have a nonmonotonic dependence on the fraction of S sites. In other words, we see a nonmonotonic dependence of the interfacial polymer dynamics on its affinity with the surface, when the latter involves some heterogeneity. The maximum activation energy belongs to the surface containing 75% S and 25% W sites, which combines near-maximum average polymer-surface interactions with near-maximum spread or disorder in these interactions. Our results have interesting implications for polymer adhesion and friction and structure-property relationships in polymer nanocomposites.

Understanding generic mechanisms of functions shared by the secretory phospholipase A2 (sPLA2) family involved in the lipid metabolism and cell signaling and the molecular basis of function specificity for family members is an intriguing but challenging problem for biologists. Here, we explore the issue through extensive analyses using a combination of structure-based methods and bioinformatics tools on130 sPLA2 family members. The principal component analysis of the structure ensemble reveals that the enzyme has an open-close motion which helps widen the substrate binding channel, facilitating its binding to phospholipid. Performing elastic network model and sequence analyses found that the residues critical for family functions, such as cysteine and catalytic residues, are highly conserved and undergo minimal movements, which is evolutionarily essential as their perturbation would impact the function, while the four residue regions involved in the association with the calcium ion/membrane are lowly conserved and of high mobility and large variations in low-to-intermediate frequency modes, which reflects the specificity of members. The analyses from perturbation response scanning also reveal that the above four regions with high sensitivity to an external perturbation are member-specific, suggesting their different roles in allosteric modulation, while the minimal sensitive residues are the shared characteristics across family members, which play an important role in maintaining structural stability as the folding core. This study is helpful for understanding how sequences, structures, and dynamics of sPLA2 family members evolve to ensure their common and specific functions and can provide a guide for accurate design of proteins with finely tuned activities.

The kinetics of photoluminescence (PL) and time-resolved emission spectra (TRES) of melanin solutions with an effective electron acceptor 2,4,7-trinitrofluorenone (TNF) have been studied. Based on ...

We study the influence of cellulose nanocrystals on the oil–water interfacial viscoelasticity and consequently on the emulsification and the three-phase (oil–water–solid) contact-line movement. Cel...

We investigated the dynamics of the topological network formed by rotaxane-type movable crosslinks consisting of a poly(ethyl acrylate) backbone threaded through peracetylated cyclodextrins, which ...

Though the strong transformation in mechanical properties of glass-forming materials such as amorphous polymers near the glass transition, Tg, has long been recognized and exploited, efforts to und...

Mitochondrial structure and organization is integral to maintaining mitochondrial homeostasis and an emerging biological target in aging, inflammation, neurodegeneration, and cancer. The study of mitochondrial structure and its functional implications remains challenging in part because of the lack of available tools for direct engagement, particularly in a disease setting. Here, we report a gold-based approach to perturb mitochondrial structure in cancer cells. Specifically, the design and synthesis of a series of tricoordinate Au(I) complexes with systematic modifications to group 15 nonmetallic ligands establish structure–activity relationships (SAR) to identify physiologically relevant tools for mitochondrial perturbation. The optimized compound, AuTri-9 selectively disrupts breast cancer mitochondrial structure rapidly as observed by transmission electron microscopy with attendant effects on fusion and fission proteins. This phenomenon triggers severe depolarization of the mitochondrial membrane in cancer cells. The high in vivo tolerability of AuTri-9 in mice demonstrates its preclinical utility. This work provides a basis for rational design of gold-based agents to control mitochondrial structure and dynamics.

Understanding the presence and dynamics of chemical pollutants in individual cells is fundamentally important for their trafficking, fate, and toxicity in humans. The presence of molecular components (i.e., proteins and mRNA) in individual cells of higher organisms is considered a stochastic event. The characteristics of chemical pollutants, as extrinsic compounds, in subpopulation of human cells on single-cell basis have not been explored yet. Here, we demonstrated the lead (Pb) content in individual mature erythrocytes (m-erythrocytes) of Pb-intoxicated patients, and healthy subjects exhibited a unified pattern in probability distribution (gamma distribution) and dynamics, despite being highly heterogeneous. The Pb content in individual m-erythrocytes decreased with the lifetime of m-erythrocytes. Meanwhile, the distribution and dynamics were found to be highly related to the Pb content in m-erythrocytes and was independent of patients and their status. This is the first study to analyze the distribution pattern of chemical pollutants at a single-cell level in higher organisms. This study sheds light on the molecular mechanism of Pb trafficking and fate in humans and the search for an efficient strategy to improve Pb excretion during Pb treatment.

Understanding the complex interplay among gasotransmitters is of great significance but remains technically challenging. In this study, we present the design and synthesis of a dually responsive BOD-NH-SC reporter for probing the dynamic and alternating existence of NO and H2 S in living cells. This designed reporter can repeatedly cycle S-nitrosation and transnitrosation reactions when successively treated with NO and H2 S, thus affording the interchange of NIR fluorescence at 645 nm (NO) and NIR II fluorescence at 936 nm (H2 S). In light of this unique fluorescence alternation between two colors, we synthesized water-soluble BOD-NH-SC dots to visualize the intracellular dynamics of NO and H2 S. These molecular probes thus provide a toolbox to elucidate the interplaying roles of NO and H2 S in the complex interaction networks of various signal transduction pathways.

The dynamics of molecules in solution is usually quantified by the determination of timescale-specific amplitudes of motions. High-resolution nuclear magnetic resonance (NMR) relaxometry experiments—where the sample is transferred to low fields for longitudinal (T1) relaxation, and back to high field for detection with residue-specific resolution—seeks to increase the ability to distinguish the contributions from motion on timescales slower than a few nanoseconds. However, tumbling of a molecule in solution masks some of these motions. Therefore, we investigate to what extent relaxometry improves timescale resolution, using the “detector” analysis of dynamics. Here, we demonstrate improvements in the characterization of internal dynamics of methyl-bearing side chains by carbon-13 relaxometry in the small protein ubiquitin. We show that relaxometry data leads to better information about nanosecond motions as compared to high-field relaxation data only. Our calculations show that gains from relaxometry are greater with increasing correlation time of rotational diffusion., Journal of Biomolecular NMR, 75 (2-3), ISSN:0925-2738, ISSN:1573-5001

Heavy metals in the water environment are known to have a negative effect on the viability of fish in early development. We have discussed the influence of environmental factors on early embryo development from the viewpoint of the correlation adaptometry method. The analysis of time series with the subsequent construction of a mathematical model was used to determine the change in the greatest effect of certain types of ions on the values of the transmembrane potential for prognostic purposes. The membrane potential is accepted as an integral indicator of the state of the embryos. Structures of five elements of the same type were constructed for the time shifts from 0 to 180 minutes. Each element in the system characterizes the value of the transmembrane potential that was measured in a cell incubated in one of the five solutions during early embryo development. Mathematical models describing the cell membrane potential dynamics have been created and studied. It was noted that the transmembrane potential dynamics of embryo cells is dependent on a change in the value of the correlation coefficient between elements of the system. A decrease in the sum of the correlations between individual elements of the system with an increase in the magnitude of the time shift is established. The results of the numerical solutions of the system equations indicated the sequence of changes in the greatest effect of the incubation medium on the value of the membrane potential in cells. The study of the membrane potentials’ dynamics, using the total values of the strength of correlation, confirmed the influence of heavy metals in the incubation medium on the membrane potential of embryo cell in early development.

We present the results from an extensive atomistic molecular dynamics simulation study of poly(ethylene oxide) (PEO) doped with various amounts of lithium-bis(trifluoromethane)sulfonimide (LiTFSI) salt under the influence of external electric field strengths up to $1\,$V/nm. The motivation stems from recent experimental reports on the nonlinear response of mobilities to the application of an electric field in such electrolyte systems and arising speculations on field-induced alignment of the polymer chains, creating channel-like structures that facilitate ion passage. Hence, we systematically examine the electric field impact on the lithium coordination environment, polymer structure as well as ionic transport properties and further present a procedure to quantify the susceptibility of both structural and dynamical observables to the external field. Our investigation reveals indeed a coiled-to-stretched transformation of the PEO strands along with a concurrent nonlinear behavior of the dynamic properties. However, from studying the temporal response of the unperturbed electrolyte system to field application we are able to exclude a structurally conditioned enhancement of ion transport and surprisingly observe a slowing down. A microscopic understanding is supplied., Main manuscript comprises 30 pages and 13 figures, supplementary information section comprises 30 pages and 28 figures

The molecular dynamics simulation using the so-called force field is a computational method to investigate the conformational stability and dynamics of various biomolecules, including proteins and nucleic acids. While a force-balanced force field is necessary for realistic simulations, recent studies revealed that all standard CHARMM and AMBER force fields over-stabilize the protein–DNA interfaces, resulting in abnormally slow diffusion of DNA-binding proteins. To address this issue, we recently developed the CUFIX corrections by calibrating the electrostatic interactions at the protein–DNA interfaces and demonstrated that the CUFIX corrections dramatically improved the diffusion dynamics of DNA-binding proteins. However, whether the improvement was achieved correctly or at the cost of abnormal destabilization of protein–DNA interactions should be validated. Here, we prove that the CUFIX corrections achieved the balance by demonstrating that the CUFIX corrections maintain the complex structure of DNA and a histone-like protein, Hbb.

An understanding of nucleation, growth and coalescence of voids is required to predict the spall fracture. We employ molecular dynamics simulations to investigate the effect of temperature on the n...

Despite being the most ubiquitous compound on Earth, the fundamental properties of water are not fully understood, especially in nanoconfinement. Densely grafted polyelectrolyte (PE) molecules atta...

Abstract Poromechanics plays a key role in modelling hard and soft tissue behaviours, by providing a thermodynamic framework in which chemo-mechanical mutual interactions among fluid and solid constituents can be consistently rooted, at different scale levels. In this context, how different biological species (including cells, extra-cellular components and chemical metabolites) interplay within complex environments is studied for characterizing the mechanobiology of tumor growth, governed by intratumoral residual stresses that initiate mechanotransductive processes deregulating normal tissue homeostasis and leading to tissue remodelling. Despite the coupling between tumor poroelasticity and interspecific competitive dynamics has recently highlighted how microscopic cells and environment interactions influence growth-associated stresses and tumor pathophysiology, the nonlinear interlacing among biochemical factors and mechanics somehow hindered the possibility of gaining qualitative insights into cells dynamics. Motivated by this, in the present work we recover the linear poroelasticity in order to benefit of a reduced complexity, so first deriving the well-known Lyapunov stability criterion from the thermodynamic dissipation principle and then analysing the stability of the mechanical competition among cells fighting for common space and resources during cancer growth and invasion. At the end, the linear poroelastic model enriched by interspecific dynamics is also exploited to show how growth anisotropy can alter the stress field in spherical tumor masses, by thus indirectly affecting cell mechano-sensing. GraphicAbstract

Biomolecules are in constant motion. To understand how they function, and why malfunctions can cause disease, it is necessary to describe their three-dimensional structures in terms of dynamic conformational ensembles. Here, we demonstrate how nuclear magnetic resonance (NMR) spectroscopy provides an essential, dynamic view of structural biology that captures biomolecular motions at atomic resolution. We focus on examples that emphasize the diversity of biomolecules and biochemical applications that are amenable to NMR, such as elucidating functional dynamics in large molecular machines, characterizing transient conformations implicated in the onset of disease, and obtaining atomic-level descriptions of intrinsically disordered regions that make weak interactions involved in liquid-liquid phase separation. Finally, we discuss the pivotal role that NMR has played in driving forward our understanding of the biomolecular dynamics-function paradigm.

The changes in the optical properties of water and hexane under femtosecond irradiation (Ti : Al2O3 laser, wavelength 800 nm, intensity ∼1013 W cm−2) are investigated in the cavitation (bubble-formation) regime using interference microscopy in a time interval of ∼1.5 ns since the impact onset. A comparison of the dynamics of radiation-induced processes (solvation of excess electrons, pair recombination, and development of precavitation processes) is performed. The excited-carrier concentration is estimated, and these estimates are found to be inconsistent with the amount of energy that must be transferred to the liquid during a pulse to implement its heating and subsequent cavitation. This inconsistency is especially pronounced for hexane, where ionisation processes can barely be detected by interferometry. The experimental results put new questions about the mechanisms of energy transfer in both polar and nonpolar liquids subjected to intense laser irradiation.

The effect of cooling on in vivo intracellular calcium ion concentration [Ca2+]i after eccentric contractions (ECs) remains to be determined. We tested the hypothesis that cryotherapy following ECs promotes an increased [Ca2+]i and induces greater muscle damage in two muscles with substantial IIb and IIx fiber populations. The thin spinotrapezius (SPINO) muscles of Wistar rats were used for in vivo [Ca2+]i imaging, and tibialis anterior (TA) muscles provided greater fidelity and repeatability of contractile function measurements. SPINO [Ca2+]i was estimated using fura 2-AM and the magnitude, location, and temporal profile of [Ca2+]i determined as the temperature near the muscle surface post-ECs was decreased from 30°C (control) to 20°C or 10°C. Subsequently, in the TA, the effect of post-ECs cooling to 10°C on muscle contractile performance was determined at 1 and 2 days after ECs. TA muscle samples were examined by hematoxylin and eosin staining to assess damage. In SPINO, reducing the muscle temperature from 30°C to 10°C post-ECs resulted in a 3.7-fold increase in the spread of high [Ca2+]i sites generated by ECs ( P < 0.05). These high [Ca2+]i sites demonstrated partial reversibility when rewarmed to 30°C. Dantrolene, a ryanodine receptor Ca2+ release inhibitor, reduced the presence of high [Ca2+] sites at 10°C. In the TA, cooling exacerbated ECs-induced muscle strength deficits via enhanced muscle fiber damage ( P < 0.05). By demonstrating that cooling post-ECs potentiates [Ca2+]i derangements, this in vivo approach supports a putative mechanistic basis for how postexercise cryotherapy might augment muscle fiber damage and decrease subsequent exercise performance.

Molecular dynamics simulations with many-body polarizable force fields were carried out to investigate the thermodynamic, structural, and dynamic properties of aqueous solutions of 1-butyl-3-methyl...

We report the effect of pH on the dynamics and structure of 3D networks formed by the temperature-dependent hydrophobic association of the end blocks of P(nBuMA18-co-TEGMA15)-b-PDMAEMA159-b-P(nBuMA...

We employ molecular dynamics simulations to investigate the evolution dynamics of {101¯2} twinning in single-crystal Ti under shock loading. The shock compression applied perpendicular to the c-axi...

The lability, dynamics of the first solvation shell, and structure breaking effect properties of Cs+ in liquid ammonia have been evaluated using Quantum Mechanical Charge Field Molecular Dynamics (...

The delocalized exciton on conjugated polymers plays a momentous role in efficient charge generation and transport processes. Because the exciton is delocalized over the conjugated backbone, the ex...

Abnormal protein aggregation in the nervous tissue leads to several neurodegenerative disorders like Alzheimer's disease (AD). In AD, accumulation of the amyloid beta (Aβ) peptide is proposed to be an early important event in pathogenesis. Significant research efforts are devoted so as to understand the Aβ misfolding and aggregation. Molecular dynamics (MD) simulations complement experiments and provide structural information at the atomic level with dynamics without facing the same experimental limitations. Artificial missense mutations are employed experimentally and computationally for providing insights into the structure-function relationships of amyloid-β in relation to the pathologies of AD. Present work describes the MD simulations for 100 ns so as to probe the structural and conformational dynamics of Aβ1-42 assemblies and its mutants. Essential dynamics analysis with respect to conformational deviation of

We employ molecular dynamics (MD) simulations to study the spreading and imbibition of a liquid drop on a porous, soft, solvophilic, and responsive surface represented by a layer of polymer molecul...

Protein hydration dynamics plays an important role in many physiological processes since protein fluctuations, slow solvation, and the dynamics of hydrating water are all intrinsically related. Red edge excitation shift (REES) is a unique and powerful wavelength-selective (i.e. excitation-energy dependent) fluorescence approach that can be used to directly monitor the environment-induced restriction and dynamics around a polar fluorophore in a complex biological system. This review is mainly focused on recent applications of REES and a novel analysis of REES data to monitor the structural dynamics, functionally relevant conformational transitions and to unmask the structural ensembles in proteins. In addition, the novel utility of REES in imaging protein aggregates in a cellular context is discussed. We believe that the enormous potential of REES approach showcased in this review will engage more researchers, particularly from life sciences.

Deubiquitinase A (DUBA) belongs to the ovarian tumor family of deubiquitinating enzymes and was initially identified as a negative regulator of type I interferons, whose overproduction has been linked to autoimmune diseases. The deubiquitinating activity of DUBA is positively regulated by phosphorylation at a single serine residue, S177, which results in minimal structural changes. We have previously shown that phosphorylation induces a two-state conformational equilibrium observed only in the active form of DUBA, highlighting the functional importance of DUBA dynamics. Here, we report the conformational dynamics of DUBA on the microsecond-to-millisecond time scales characterized by nuclear magnetic resonance relaxation dispersion experiments. We found that motions on these time scales are highly synchronized in the phosphorylated and nonphosphorylated DUBA. Despite the overall similarity of these two forms, different dynamic properties were observed in helix α1 and the neighboring regions, including residue S177, which likely contribute to the activation of DUBA by phosphorylation. Moreover, our data suggest that transient unfolding of helix α6 drives the global conformational process and that mutations can be introduced to modulate this process, which provides a basis for future studies to define the exact functional roles of motions in DUBA activation and substrate specificity.

The dynamics of different blocks in block copolymers are expected to affect the other blocks due to compositional heterogeneity, thus influencing their bulk structure and performance. It is signifi...

Direct dynamics simulations with the M06/6-311++G(d,p) level of theory were performed to study the 3CH2 + 3O2 reaction at 1000 K temperature on the ground state singlet surface. The reaction is complex with formation of many different product channels in highly exothermic reactions. CO, CO2, H2O, OH, H2, O, H, and HCO are the products formed from the reaction. The total simulation rate constant for the reaction at 1000 K is (1.2 ± 0.3) × 10-12 cm3 molecule-1 s-1, while the simulation rate constant at 300 K is (0.96 ± 0.28) × 10-12 cm3 molecule-1 s-1. The simulated product yields show that CO is the dominant product and the CO:CO2 ratio is 5.3:1, in good comparison with the experimental ratio of 4.3:1 at 1000 K. On comparing the product yields for the 300 and 1000 K simulations, we observed that, except for CO and H2O, the yields of the other products at 1000 K are lower at 300 K, showing a negative temperature dependence.

Cells continuously sense and react to mechanical cues from their surrounding matrix, which consists of a fibrous network of biopolymers that influences their fate and behavior. Several powerful methods employing magnetic control have been developed to assess the micromechanical properties within extracellular matrix (ECM) models hosting cells. However, many of these are limited to in-plane sensing and actuation, which does not allow the matrix to be probed within its full 3D context. Moreover, little attention has been given to factors specific to the model ECM systems that can profoundly influence the cells contained there. Here we present methods to spatiotemporally probe and manipulate extracellular matrix networks at the scale relevant to cells using magnetic microprobes (mu Rods). Our techniques leverage 3D magnetic field generation, physical modeling, and image analysis to examine and apply mechanical stimuli to fibrous collagen matrices. We determined shear moduli ranging between hundreds of Pa to tens of kPa and modeled the effects of proximity to rigid surfaces and local fiber densification. We analyzed the spatial extent and dynamics of matrix deformation produced in response to magnetic torques on the order of 10 pNm, deflecting fibers over an area spanning tens of micrometers. Finally, we demonstrate 3D actuation and pose extraction of fluorescently labelled mu Rods., Lab on a Chip, 21 (20), ISSN:1473-0197, ISSN:1473-0189

Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction. Here, we report the molecular basis of a human mutation in cTnC's αD-helix (TNNC1-p.C84Y) that impacts conformational dynamics of the D/E central-linker and sampling of discrete states in the N-domain, favoring the “primed” state associated with Ca2+ binding. We demonstrate cTnC's αD-helix normally functions as a central hub that controls minimally frustrated interactions, maintaining evolutionarily conserved rigidity of the N-domain. αD-helix perturbation remotely alters conformational dynamics of the N-domain, compromising its structural rigidity. Transgenic mice carrying this cTnC mutation exhibit altered dynamics of sarcomere function and hypertrophic cardiomyopathy. Together, our data suggest that disruption of evolutionary conserved molecular frustration networks by a myofilament protein mutation may ultimately compromise contractile performance and trigger hypertrophic cardiomyopathy., Cardiac TnC (cTnC) is highly conserved among mammals, and genetic variants can result in disease by perturbing Ca2+-regulation of myocardial contraction.

The vibrational- and rotational-mode specificity of the multichannel NH+ + H2 reaction is studied on a recently constructed ab initio-based global potential energy surface using an initial state selected quasi-classical trajectory method, and the trajectories are analyzed using an isometric feature mapping and k-means approach. All excitation modes promote two reactions (R1: NH′+ + H2 → NH+ + HH′ and R4: NH′+ + H2 → NH2+ + H′) where both NH and HH bonds are broken, but reduce the reactivity of the proton-transfer reaction R2 (NH′+ + H2 → N + H′H2+) at low collision energies. For the hydrogen-transfer reaction R3 (NH′+ + H2 → HNH′+ + H), the rotational excitation of NH+ enhances the reactivity remarkably, while its vibrational excitation has an inhibiting effect on the reaction. The trajectory analyses show that the vibrational and rotational excitations of NH+ make R3 tend to go over a submerged saddle point instead of extracting hydrogen atoms directly. On the other hand, the motions of the H2 reactant facilitate the enhancement of the reactivity but they do not affect the mechanism of R3. In addition, the results suggest that the coupling of the isometric feature mapping and the k-means approach in the trajectory analysis is an appropriate tool for reaction-dynamics studies.