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The mechanical interaction between cells and the extracellular matrix (ECM) is fundamental to coordinate collective cell behavior in tissues. Relating individual cell-level mechanics to tissue-scale collective behavior is a challenge that cell-based models such as the cellular Potts model (CPM) are well-positioned to address. These models generally represent the ECM with mean-field approaches, which assume substrate homogeneity. This assumption breaks down with fibrous ECM, which has nontrivial structure and mechanics. Here, we extend the CPM with a bead-spring model of ECM fiber networks modeled using molecular dynamics. We model a contractile cell pulling with discrete focal adhesion-like sites on the fiber network and demonstrate agreement with experimental spatiotemporal fiber densification and displacement. We show that at high network cross-linking, contractile cell forces propagate over at least eight cell diameters, decaying with distance with power law exponent n= 0.35 - 0.65 typical of viscoelastic ECMs. Further, we use in silico atomic force microscopy to measure local cell-induced network stiffening consistent with experiments. Our model lays the foundation for investigating how local and long-ranged cell-ECM mechanobiology contributes to multicellular morphogenesis., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

We analyze an 'up-the-gradient' model for the formation of transport channels of the phytohormone auxin, through auxin-mediated polarization of the PIN1 auxin transporter. We show that this model admits a family of travelling wave solutions that is parameterized by the height of the auxin-pulse. We uncover scaling relations for the speed and width of these waves and verify these rigorous results with numerical computations. In addition, we provide explicit expressions for the leading-order wave profiles, which allows the influence of the biological parameters in the problem to be readily identified. Our proofs are based on a generalization of the scaling principle developed by Friesecke and Pego to construct pulse solutions to the classic Fermi-Pasta-Ulam-Tsingou model, which describes a one-dimensional chain of coupled nonlinear springs., (© 2022. The Author(s).)

The relation between the chemical structure and the mechanical behavior of molecular machines is of paramount importance for a rational design of superior nanomachines. Here, we report on a mechanistic study of a nanometer scale translational movement in two bistable rotaxanes. Both rotaxanes consist of a tetra-amide macrocycle interlocked onto a polyether axle. The macrocycle can shuttle between an initial succinamide station and a 3,6-dihydroxy- or 3,6-di- tert -butyl-1,8-naphthalimide end stations. Translocation of the macrocycle is controlled by a hydrogen-bonding equilibrium between the stations. The equilibrium can be perturbed photochemically by either intermolecular proton or electron transfer depending on the system. To the best of our knowledge, utilization of proton transfer from a conventional photoacid for the operation of a molecular machine is demonstrated for the first time. The shuttling dynamics are monitored by means of UV-vis and IR transient absorption spectroscopies. The polyether axle accelerates the shuttling by ∼70% compared to a structurally similar rotaxane with an all-alkane thread of the same length. The acceleration is attributed to a decrease in activation energy due to an early transition state where the macrocycle partially hydrogen bonds to the ether group of the axle. The dihydroxyrotaxane exhibits the fastest shuttling speed over a nanometer distance (τ shuttling ≈ 30 ns) reported to date. The shuttling in this case is proposed to take place via a so-called harpooning mechanism where the transition state involves a folded conformation due to the hydrogen-bonding interactions with the hydroxyl groups of the end station.

Synthetic molecular machines are promising building blocks for future nanoscopic devices. However, the details of their mechanical behaviour are in many cases still largely unknown. A deeper understanding of mechanics at the molecular level is essential for the design and construction of complex nanodevices. Here, we show that transient two-dimensional infrared (T2DIR) spectroscopy makes it possible to monitor the conformational changes of a translational molecular machine during its operation. Translation of a macrocyclic ring from one station to another on a molecular thread is initiated by a UV pulse. The arrival of the shuttling macrocycle at the final station is visible from a newly appearing cross peak between these two moieties. To eliminate spectral congestion in the T2DIR spectra, we use a subtraction method applicable to many other complex molecular systems. The T2DIR spectra indicate that the macrocycle adopts a boat-like conformation at the final station, which contrasts with the chair-like conformation at the initial station.

Background: Early detection and treatment of STI/HIV are public health priorities. Our objective was to compare characteristics of men who have sex with men (MSM) in Dutch data available in 2010 from EMIS, an international internet survey, Schorer Monitor, a Dutch internet survey, and data from STI- clinic visits, since these might be subject to different and unknown biases., Methods: Data from Dutch MSM Internet Surveys (EMISNL N = 3,787; Schorer Monitor, SMON N = 3,602), and 3,800 STI clinic visits (SOAP) were combined into one dataset. We included factors that were measured in all three databases. The socio-demographics included were age (at the time of the survey), zip code, and ethnicity. Behavioural variables included were the number of sexual partners, condom use with last sexual partner, drug use, being diagnosed with STI, being diagnosed with HIV, and HIV testing. Outcomes we investigated were being diagnosed with STI, HIV, and never been tested for HIV., Results: Logistic regressions showed that determinants for being diagnosed with STI were having more sexual partners, drug use, and having had an HIV test (aORs 1.3 to 17.1) in EMIS and SMON. Determinants for being diagnosed with HIV in all three databases were older age, living in Amsterdam, and having more partners (aORs 1.8 to 4.4). In EMIS and SMON, drug use, non-condom use, and having STI were additional determinants (aORs 1.6 to 8.9). Finally, determinants associated with never been tested for HIV were being younger (only SOAP), living outside of Amsterdam, having fewer partners, no drug use, and no STI (aORs 0.2 to 0.8)., Conclusions: Risk factors from internet surveys were largely similar, but differed from STI clinics, possibly because it involves self-reports rather than diagnoses or because of differences in timing. The difference between the internet surveys and STI clinic data is much less pronounced for having never been tested, suggesting both are appropriate for this outcome. These findings shed light on conclusions drawn from different data sources, as well as the comparability of recruitment strategies, the robustness of risk factors, consequences of phrasing questions differently, and on (policy) implications based on different data sources.

Complex formation and intermolecular excited-state proton transfer (ESPT) between a dihydroxy-1,8-naphthalimide photoacid and organic bases are investigated in polar aprotic solvents. First, quantum chemical calculations are used to explore the acid-base and spectroscopic properties and to identify energetically favorable complexes. The two hydroxyl groups of the photoacid enable stepwise formation of 1 : 1 and 1 : 2 complexes. Weak bases exhibit only hydrogen-bonding interactions whereas strong bases are able to deprotonate one of the hydroxyl groups resulting in strong negative cooperativity (K1≫ 4K2) in the formation of the 1 : 2 complex. Time-resolved fluorescence studies of the complexes provide strong indications of a three-step dissociation process. The species involved in the model are: a hydrogen-bonded complex, a hydrogen-bonded ion pair, a solvent separated ion pair, and a free ion pair.

The ground- and excited-state acid-base properties of three novel naphthalimide-based “super” photoacids were studied using steady-state and time-resolved spectroscopy. The compounds exhibit pKa = 8.8-8.0 and pKa* = -1.2 to -1.9. The decrease in both ground- and excited-state pKa is achieved by attachment of an electron withdrawing group (sulfonate) on the aromatic system. All compounds are deprotonated upon excitation in alcohols and DMSO. Good correlation is established between the pKa* and the ratio of the neutral and anion emission intensities in a certain solvent. The excited-state intermolecular proton transfer to solvent (H2O and DMSO) is explained by a two-step model. In the first step, short-range proton transfer takes place, resulting in the formation of a contact ion pair. Free ion pairs are formed in the diffusion controlled second step.

We report on experimental high-resolution spectroscopic studies in combination with ab initio computational studies that investigate the excited-state dynamics of methyl-4-hydroxycinnamate thioester and (5-hydroxyindan-(1E)-ylidene)acetic acid, derivatives of the photoactive yellow protein (PYP) chromophore. These studies aim to elucidate (a) how the thioester moiety influences the photophysics and photochemistry of the p-coumaric acid chromophore and (b) to what extent rotation of the single bond adjacent to the phenyl ring is involved in the decay dynamics of the electronically excited states. The experimental studies show that sulfur substitution leads to broad, unstructured excitation spectra that contrast sharply with the well-resolved spectra of compounds with an oxygen-based ester. Furthermore, internal conversion to the lower-lying nπ* state is absent. The absence of this decay channel is rationalized by quantum-chemical calculations that reveal that in the nπ* state of the thio compounds the molecule exhibits a large out-of-plane "kink" at the sulfur atom. Franck-Condon simulations of the excitation spectra of the V(ππ*) state highlight the activity of various vibrational modes in the neutral chromophore and indicate that upon sulfur substitution internal conversion to the ground state occurs at a significantly higher rate. The similarities observed in the excitation spectra and decay dynamics of the locked and unlocked compounds suggest that in the present experiments single-bond torsion does not show up prominently. The conclusion that for the isolated molecule double-bond torsion is dominating the excited-state dynamics is tentatively confirmed by the quantum-chemical calculations.

The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the 'lubricant of life'.

An optically transparent thin-layer electrochemical (OTTLE) cell with a locally extended optical path has been developed in order to perform vibrational circular dichroism (VCD) spectroscopy on chiral molecules prepared in specific oxidation states by means of electrochemical reduction or oxidation. The new design of the electrochemical cell successfully addresses the technical challenges involved in achieving sufficient infrared absorption. The VCD-OTTLE cell proves to be a valuable tool for the investigation of chiral redox-active molecules.

We report on experimental high-resolution spectroscopic studies in combination with advanced theoretical calculations that focus on the excited-state dynamics of various forms of the chromophore of the Photoactive Yellow Protein (PYP), and the dependence of these dynamics on conformational and isosteric structure, as well as the biological environment. Three-colour nanosecond multiphoton ionization pump-probe studies confirm and extend previous conclusions that the dominant decay channel of the lowest excited pipi* state (the so-called V' state) of methyl-4-hydroxycinnamate is picosecond internal conversion to the adiabatically lower nPi* state, and enable us to resolve apparent contradictions with picosecond pump-probe studies. Comparison of multiphoton ionization and laser induced fluorescence excitation spectra leads to the assignment of the hitherto elusive excitation spectrum of the V(pipi*) state. Complexation of methyl-4-hydroxycinnamate with water radically changes the excited-state dynamics; internal conversion to the npi* state is absent, and bond isomerization channels instead play a prominent role. Excited states of the thio-ester compound, the form in which the chromophore is present in PYP, have till the present study remained out of reach of gas-phase studies. The excitation spectra obtained here show a broad, almost structureless band system, giving evidence for enhanced nonradiative decay channels. The gas-phase results will be discussed in the context of results from ultrafast studies on these two chromophores in solution.

Time-resolved vibrational spectroscopy is used to investigate the inter-component motion of an ultraviolet-triggered two-station molecular shuttle. The operation cycle of this molecular shuttle involves several intermediate species, which are observable in the amide I and amide II regions of the mid-IR spectrum. Using ab initio calculations on specific parts of the rotaxane, and by comparing the transient spectra of the normal rotaxane with that of the N-deuterated version, we can assign the observed vibrational modes of each species occurring during the shuttling cycle in an unambiguous way. The complete time- and frequency-dependent data set is analyzed using singular value decomposition (SVD). Using a kinetic model to describe the time-dependent concentrations of the transient species, we derive the absorption spectra associated with each stage in the operation cycle of the molecular shuttle, including the recombination of the charged species.

Vibrational circular dichroism is a powerful technique to study the stereochemistry of chiral molecules, but often suffers from small signal intensities. Electrochemical modulation of the energies of the electronically excited state manifold is now demonstrated to lead to an order of magnitude enhancement of the differential absorption. Quantum-chemical calculations show that increased mixing between ground and excited states is at the origin of this amplification., (This journal is © The Royal Society of Chemistry 2012)

To design more effective CIEEL (chemically initiated electron exchange luminescence) systems demands a complete picture of the dynamics of the chemiluminescence, which is often a challenge. In this work, photoluminescence of the methyl m-oxybenzoate anion - the authentic emitter of AMPPD (3-[2-spiroadamantane]-4-methoxy-4-[3-phosphoryloxy]-phenyl-1,2-dioxetane) in aqueous solvent has been studied. Combining the effect of solvent properties, e.g. pH value, and spectroscopic studies employing steady-state and ultrafast time-resolved emission and absorption and (1)H NMR techniques, a novel mechanism is proposed. We conclude that the deviation of emission peaks between chemiluminescence and photoluminescence of the authentic emitter of AMPPD i.e. the methyl m-oxybenzoate anion, in alkaline aqueous solvents is due to its hydrolysis, rather than the hydrogen-bonding effect as has been assumed so far. Besides, the hydrogen-bonding is suggested to play a key role in significantly decreasing the chemiluminescence yield of AMPPD in aqueous solution by shortening the lifetime of the excited authentic emitter to 10 ps order of magnitude - three orders of magnitude shorter than the previously reported value ( approximately 10 ns). These results shed light on the chemiluminescence dynamics of AMPPD and facilitate the design of more effective CIEEL systems.

Rotaxanes comprise macrocycles that can shuttle between docking stations along an axle. We explored the nanosecond shuttling mechanism by reversing the relative binding affinities of two stations through ultraviolet-induced transient reduction. We monitored the ensuing changes in the CO-stretching bands of the two stations and the shuttling macrocycle by means of an infrared probing pulse. Because hydrogen-bond scission and formation at the initial and final stations led to well-resolved changes in the respective CO-stretch frequencies, the departure and arrival of the macrocycle could be observed separately. We found that the shuttling involves two steps: thermally driven escape from the initial station, followed by rapid motion along the track ending either at the initial or final station. By varying the track's length, we found that the rapid motion approximates a biased one-dimensional random walk. However, surprisingly, the direction of the overall motion is opposite that of the bias.

It has recently become possible to synthesize mechanical devices the size of a single molecule. Although it is tempting to regard such molecular machines as nanoscale versions of their macroscopic analogs, many notions from macroscopic mechanics no longer apply at a molecular level. For instance, the concept of viscous friction is meaningless for a molecular machine because the size of the solvent molecules that cause the friction is comparable to that of the machine itself. Furthermore, in many cases, the interactions between a molecular machine and its surroundings are comparable to the force driving the machine. As a result, a certain amount of intrinsic randomness exists in the motion of molecular machines, and the details of their mechanics are largely unknown. For a detailed understanding of the mechanical behavior of molecular machines, experiments that probe their motion on an ultrafast time scale, such as two-dimensional (2D) vibrational spectroscopy, are essential. This method uses coupling between vibrational modes in a molecule to investigate the molecular conformation. The coupling shows up as off-diagonal peaks in a 2D graph of the vibrational response of the molecule, analogous to the spin coupling observed in multidimensional NMR spectroscopy. Both spin coupling and vibrational coupling are sensitive probes of the molecular conformation, but 2D vibrational spectroscopy shows orders of magnitude better time resolution than NMR. In this Account, we use 2D vibrational spectroscopy to study molecular machines based on rotaxanes. These devices consist of a linear thread and a macrocycle that is noncovalently locked onto the thread. In the rotaxanes we study, the macrocycle and the thread both contain CO and NH groups. By determining the coupling between the stretching modes of these goups from the cross peaks in the 2D spectrum, we directly and quantitatively probe the relative position and orientation of the macrocycle and the thread for both a small model rotaxane and a rotaxane-based molecular shuttle. Our results demonstrate the feasibility of using time-resolved 2D-IR experiments to measure externally triggered structural changes of molecular devices with subpicosecond time resolution. We can observe each of the elementary events that underlie the mechanical motion separately. With this ability to investigate the nature of the mechanical motions at the molecular level and with unprecedented time resolution, we expect that 2D-IR spectroscopy on molecular machines will lead to new insights into their function.

Femtosecond transient absorption spectroscopy was employed to determine quantitatively the ultrafast S1-T1 intersystem crossing in a 2-substituted 9,10-anthraquinone derivative (3), kisc = 2.5 x 10(12) s-1. Notwithstanding this rapid process, photoexcitation of dyad 1 is followed by competition between intersystem crossing and intramolecular charge separation, the latter leading to a short-lived (2 ps) singlet charge-transfer (CT) state. The local triplet state itself undergoes slower charge separation to populate a relatively long-lived (130 ns) triplet CT state. An earlier report about the formation of an extremely long-lived CT state (> 900 micros) in 1 was found to be erroneous and was related to the sacrificial photo-oxidation of the dimethylsulfoxide solvent used in that study. Finally, some important criteria have been formulated for future experimental validation of "unusually long-lived" CT states.

1. In urine of rats treated with 1',2'-epoxyhexobarbital, unchanged compound and six metabolites were identified: 1,5-dimethylbarbituric acid, which is the end product of an epoxide-diol pathway, two stereochemically different 3'-hydroxy-1',2'-epoxyhexobarbitals, a hydroxyfuropyrimidine, 3'-hydroxyhexobarbital and 3'-ketohexobarbital. 2. The analytical methods used were based on capillary g.l.c. with nitrogen-selective or mass spectrometric detection. Identification was by electron impact and chemical ionization mass spectrometry. All the reference compounds needed for comparison were synthesized. 3. The mean plasma elimination half-life of 1',2'-epoxyhexobarbital after intra-arterial administration to the rat was 13.7 +/- 1.5 min (mean +/-S.D.; n = 3). A total body clearance of 35.2 +/- 9.6 ml/min (mean +/- S.D.) was calculated, which includes renal clearance of unchanged epoxide. 4. In rat liver microsomal preparations it was demonstrated that 1',2'-epoxyhexobarbital is hydrated by epoxide hydratase. With 1 mM 1,1,1,-trichloropropene-2,3-oxide (TCPO) this enzymic reaction could be inhibited completely. 5. On administration of the individual metabolites of the epoxide to rats, no evidence was found for their possible intermediacy in the formation of 3'-hydroxy- or 3'-ketohexobarbital, which are major metabolites of hexobarbital.

1. In urine of rats given vinylbital (5-vinyl-5-(1'-methylbutyl)barbituric acid) i.p., unchanged vinylbital and its devinylated metabolite, 5-(1'-methylbutyl)barbituric acid, were identified. Rats synthetic 1',2'-epoxyvinylbital excreted the same compound as a major metabolite. No unchanged epoxide, nor 1',2'-dihydroxyvinylbital, could be identified in the urine of rats treated with vinylbital or its epoxide. 2. Attempts to synthesize 1',2'-dihydroxyvinylbital from 1',2'-epoxyvinylbital by acidic hydrolysis revealed that this possible metabolite decomposes readily to 5-(1'-methylbutyl)barbituric acid by a 'retro-aldol type' reaction. 3. In rat liver microsomal preparation 1',2'-epoxyvinylbital is readily hydrated by epoxide hydratase, but this reaction is almost completely inhibited by 0.8 mM 1,1,1-trichloropropene-2,3-oxide (TCPO). This finding and the identification of 5-(1'-methylbutyl)barbituric acid as end-product of this enzyme reaction provides further evidence for the existence of an epoxide-diol pathway in the metabolism of vinylbital. 4. Vinylbital and its devinylated metabolite are excreted in 36 h urine of rats treated with vinylbital, to an extent of 0.6 +/- 1.7% of the dose (n = 5), respectively. Upon administration of 1',2-epoxyvinylbital, 59.8 +/- 14.2% of the dose (n = 5) was excreted as 5-(1'-methylbutyl)barbituric acid. 5. In 60 h urine of three human volunteers who had taken 150 mg of vinylbital orally, 2.6 +/- 1.7% of the dose was excreted as vinylbitaland 11.0 +/- 4.1% as 5-(1'-methylbutyl) barbituric acid, illustrating that also in humans the epoxide-diol pathway plays a role in the metabolism of vinylbital.