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Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. Exact simulation of reactions in these systems is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. In this work, we experimentally simulate a paradigmatic model of molecular electron transfer using a multi-species trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. We employ the ground-state qubit of one ion to simulate the electronic degree of freedom and the optical qubit of another ion to perform reservoir engineering on a collective mode encoding a reaction coordinate. We observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. The setup allows access to the electron transfer dynamics in the non-perturbative regime, where there is no clear hierarchy among the energy scales in the model, as has been suggested to be optimal for many rate phenomena, including photosynthesis. Our results provide a testing ground for increasingly rich models of molecular excitation transfer processes that are relevant for molecular electronics and light-harvesting systems.

Protein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across 38 abundant and conserved protein families. Taking advantage of genomic exon-intron organization and extensive protein sequence data, we explore exon boundary conservation and assess their foldon-like behavior using energy landscape theoretic measurements. We found deviations in exon size distribution from exponential decay indicating selection in evolution. We describe that there is a pronounced independent foldability of segments corresponding to conserved exons, supporting the exon-foldon correspondence. We further develop a systematic partitioning of protein domains using exon boundary hot spots, unveiling minimal common exons consisting of uninterrupted alpha and/or beta elements for the majority but not all of the studied families., Comment: 18 pages, 4 figures, 8 suppl figures

Understanding structural glasses using the Random First Order Transition theory requires a description in both real space and in time, taking into account sample history. A variety of nonlinear objects enter this description, in field theory terms, when there is replica symmetry breaking: instantons, strings, flames and flows. We focus on this real space description and use it to describe the crossover to the energy landscape regime, dynamical heterogeneity, aging and the formation of shear bands in glasses under stress., Comment: This manuscript will appear in the book "Spin Glass Theory and Far Beyond - Replica Symmetry Breaking after 40 Years"

Out-of-time-order correlators (OTOCs) can be used to probe how quickly a quantum system scrambles information when the initial conditions of the dynamics are changed. In sufficiently large quantum systems, one can extract from the OTOC the quantum analog of the Lyapunov coefficient that describes the time scale on which a classical chaotic system becomes scrambled. OTOCs have been applied only to a very limited number of toy models, such as the SYK model connected with black hole information scrambling, but they could find much wider applicability for information scrambling in quantum systems that allow comparison with experiments. The vibrations of polyatomic molecules are known to undergo a transition from regular dynamics at low energy to facile energy flow at sufficiently high energy. Molecules therefore represent ideal quantum systems to study scrambling in many-body systems of moderate size (here 6 to 36 degrees of freedom). By computing quantum OTOCs and their classical counterparts we quantify how information becomes 'scrambled' quantum mechanically in molecular systems. Between early 'ballistic' dynamics, and late 'saturation' of the OTOC when the full density of states is explored, there is indeed a regime where a quantum Lyapunov coefficient can be defined for all molecules in this study. Comparison with experimental rate data shows that slow scrambling as measured by the OTOC can reach the time scale of molecular reaction dynamics. Even for the smallest molecules we discuss, the Maldacena bound remains satisfied by regularized OTOCs, but not by unregularized OTOCs, highlighting that the former are more useful for discussing information scrambling in this type of moderate-size quantum system.

Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of information not to one but to many genes carrying out distinct functions whose dynamical binding and unbinding characteristics are widely distributed. In such broadcasting networks, the intended target sites are also often dwarfed in number by the even more numerous non-functional binding sites. Taking the genetic regulatory network of NF\k{appa}B as an exemplary system we explore the impact of having numerous distributed sites on the stochastic dynamics of oscillatory broadcasting genetic networks pointing out how resonances in binding cycles control the network's specificity and performance. We also show that active kinetic regulation of binding and unbinding through molecular stripping of DNA bound transcription factors can lead to a higher coherence of gene co-expression and synchronous clearance., Comment: 13 pages, 4 figures

We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is visualized highlighting the energetic conflicts or the concordance of the local interactions in that structure. Minimally frustrated linkages highlight the stable folding core of the molecule. Sites of high local frustration, in contrast, often indicate functionally relevant regions such as binding, active or allosteric sites., Comment: 17 pages, 3 figures. Part of a Methods in Molecular Biology book on Protein Folding and Stability

Apart from not having crystallized, supercooled liquids can be considered as being properly equilibrated and thus can be described by a few thermodynamic control variables. In contrast, glasses and other amorphous solids can be arbitrarily far away from equilibrium and require a description of the history of the conditions under which they formed. In this paper we describe how the locality of interactions intrinsic to finite-dimensional systems affects the stability of amorphous solids far off equilibrium. Our analysis encompasses both structural glasses formed by cooling and colloidal assemblies formed by compression. A diagram outlining regions of marginal stability can be adduced which bears some resemblance to the quasi-equilibrium replica meanfield theory phase diagram of hard sphere glasses in high dimensions but is distinct from that construct in that the diagram describes not true phase transitions but kinetic transitions that depend on the preparation protocol. The diagram exhibits two distinct sectors. One sector corresponds to amorphous states with relatively open structures, the other to high density, more closely-packed ones. The former transform rapidly owing to there being motions with no free energy barriers; these motions are string-like locally. In the dense region, amorphous systems age via compact activated reconfigurations. The two regimes correspond, in equilibrium, to the collisional or uniform liquid and the so called landscape regime, respectively. These are separated by a spinodal line of dynamical crossovers. Owing to the rigidity of the surrounding matrix in the landscape, high-density part of the diagram, a sufficiently rapid pressure quench adds compressive energy which also leads to an instability toward string-like motions with near vanishing barriers. (SEE REST OF ABSTRACT IN THE ARTICLE.), Comment: submitted to J Phys Chem B

Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful catalysis, are examples of basic chemical activities that the great majority of polypeptides do not display, and are thought to be the outcome of the natural history of proteins. Function, a concept genuine to Biology, is at the core of evolution and often conflicts with the physical constraints. Locating the frustration between discrepant goals in a recurrent system leads to fundamental insights about the chances and necessities that shape the encoding of biological information., Comment: 17 pages, 1 figure, submitted to COSB

We derive an unbiased information theoretic energy landscape for chromosomes at metaphase using a maximum entropy approach that accurately reproduces the details of the experimentally measured pair-wise contact probabilities between genomic loci. Dynamical simulations using this landscape lead to cylindrical, helically twisted structures reflecting liquid crystalline order. These structures are similar to those arising from a generic ideal homogenized chromosome energy landscape. The helical twist can be either right or left handed so chiral symmetry is broken spontaneously. The ideal chromosome landscape when augmented by interactions like those leading to topologically associating domain (TAD) formation in the interphase chromosome reproduces these behaviors. The phase diagram of this landscape shows the helical fiber order and the cylindrical shape persist at temperatures above the onset of chiral symmetry breaking which is limited by the TAD interaction strength.

Several recent experiments suggest that rather generally the diffusion of enzymes may be augmented through their activity. We demonstrate that such swimming motility can emerge from the interplay between the enzyme energy landscape and the hydrodynamic coupling of the enzyme to its environment. Swimming thus occurs during the transit time of a transient allosteric change. We estimate the velocity during the transition. The analysis of such a swimming motion suggests the final stroke size is limited by the hydrodynamic size of the enzyme. This limit is quite a bit smaller than the values that can be inferred from the recent experiments. We also show that one proposed explanation of the experiments based on reaction heat effects can be ruled out using an extended hydrodynamic analysis. These results lead us to propose an alternate explanation of the fluorescence correlation measurements.

Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from gene state switching, a single molecule event. Stochastic dynamics of gene regulatory circuits appears to be largely responsible for bifurcations into a set of multi-attractor states that encode different cell phenotypes. The interplay of dichotomous single molecule gene noise with the nonlinear architecture of genetic networks generates rich and complex phenomena. In this paper we elaborate on an approximate framework that leads to simple hybrid multi-scale schemes well suited for the quantitative exploration of the steady state properties of large-scale cellular genetic circuits.Through a path sum based analysis of trajectory statistics we elucidate the connection of these hybrid schemes to the underlying master equation and provide a rigorous justification for using dichotomous noise based models to study genetic networks. Numerical simulations of circuit models reveal that the contribution of the genetic noise of single molecule origin to the total noise is significant for a wide range of kinetic regimes.

Cytoskeletal networks, which are essentially motor-filament assemblies, play a major role in many developmental processes involving structural remodeling and shape changes. These are achieved by nonequilibrium self-organization processes that generate functional patterns and drive intracellular transport. We construct a minimal physical model that incorporates the coupling between nonlinear elastic responses of individual filaments and force-dependent motor action. By performing stochastic simulations we show that the interplay of motor processes, described as driving anti-correlated motion of the network vertices, and the network connectivity, which determines the percolation character of the structure, can indeed capture the dynamical and structural cooperativity which gives rise to diverse patterns observed experimentally. The buckling instability of individual filaments is found to play a key role in localizing collapse events due to local force imbalance. Motor-driven buckling-induced node aggregation provides a dynamic mechanism that stabilizes the two dimensional patterns below the apparent static percolation limit. Coordinated motor action is also shown to suppress random thermal noise on large time scales, the two dimensional configuration that the system starts with thus remaining planar during the structural development. By carrying out similar simulations on a three dimensional anchored network, we find that the myosin-driven isotropic contraction of a well-connected actin network, when combined with mechanical anchoring that confers directionality to the collective motion, may represent a novel mechanism of intracellular transport, as revealed by chromosome translocation in the starfish oocyte., Comment: 11 pages, 5 figures

We compare dynamical heterogeneities in equilibrated supercooled liquids and in the nonequilibrium glassy state within the framework of the random first order transition theory. Fluctuating mobility generation and transport in the glass are treated by numerically solving stochastic continuum equations for mobility and fictive temperature fields that arise from an extended mode coupling theory containing activated events. Fluctuating spatiotemporal structures in aging and rejuvenating glasses lead to dynamical heterogeneity in glasses with characteristics distinct from those found in the equilibrium supercooled liquid. The non-Gaussian distribution of activation free energies, the stretching exponent $\beta$, and the growth of characteristic lengths are studied along with the four-point correlation function. Asymmetric thermodynamic responses upon heating and cooling are predicted to be the results of the heterogeneity and the out-of-equilibrium behavior of glasses below $T_g$. Numerical results agree with experimental calorimetry. We numerically confirm the prediction of Lubchenko and Wolynes in the glass that the dynamical heterogeneity can lead to noticeably bimodal distributions of local fictive temperatures which explains in a unified way recent experimental observations that have been interpreted as coming from two distinct equilibration mechanisms in glasses., Comment: 30 pages, 10 figures

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology., Comment: 97 pages, 30 figures

We compute the temperature-dependent barrier for alpha-relaxations in several liquids, without adjustable parameters, using experimentally determined elastic, structural, and calorimetric data. We employ the random first order transition(RFOT) theory, in which relaxation occurs via activated reconfigurations between distinct, aperiodic minima of the free energy. Two different approximations for the mismatch penalty between the distinct aperiodic states are compared, one due to Xia and Wolynes, which scales universally with temperature as for hard spheres, and one due to Rabochiy and Lubchenko, which employs measured elastic and structural data for individual substances. The agreement between the predictions and experiment is satisfactory, given the uncertainty in the measured experimental inputs. The explicitly computed barriers are used to calculate the glass transition temperature for each substance---a kinetic quantity---from the static input data alone. The temperature dependence of both the elastic and structural constants enters the temperature dependence of the barrier over an extended range to a degree that varies from substance to substance. The lowering of the configurational entropy, however, seems to be the dominant contributor to the barrier increase near the laboratory glass transition, consistent with previous experimental tests of the RFOT theory using the XW approximation. In addition, we compute the temperature dependence of the dynamical correlation length, also without using adjustable parameters. These agree well with experimental estimates obtained using the Berthier et al. procedure. Finally, we find the temperature dependence of the complexity of a rearranging region is consistent with the picture based on the RFOT theory but is in conflict with the assumptions of the Adam-Gibbs and "shoving" scenarios for the viscous slowing down in supercooled liquids., Comment: submitted to J Phys Chem B

In the context of the random first order transition theory we use an extended mode coupling theory of the glass transition that includes activated events to account for spatiotemporal structures in aging and rejuvenating glasses. We numerically solve fluctuating dynamical equations for mobility and fictive temperature fields which capture both mobility generation through activated events and facilitation effects. Upon rejuvenating, a source of high mobility at a glass surface initiates a growth front of mobility which propagates into the unstable low mobility region. The speed of the front is consistent with experiments on the rejuvenation of stable glasses, which "melt" from their surface., Comment: 4 pages, 2 figures

Signatures of glassy dynamics have been identified experimentally for a rich variety of materials in which molecular networks provide rigidity. Here we present a theoretical framework to study the glassy behavior of both passive and active network materials. We construct a general microscopic network model that incorporates nonlinear elasticity of individual filaments and steric constraints due to crowding. Based on constructive analogies between structural glass forming liquids and random field Ising magnets implemented using a heterogeneous self-consistent phonon method, our scheme provides a microscopic approach to determine the mismatch surface tension and the configurational entropy, which compete in determining the barrier for structural rearrangements within the random first order transition theory of escape from a local energy minimum. The influence of crosslinking on the fragility of inorganic network glass formers is recapitulated by the model. For active network materials, the mapping, which correlates the glassy characteristics to the network architecture and properties of nonequilibrium motor processes, is shown to capture several key experimental observations on the cytoskeleton of living cells: Highly connected tense networks behave as strong glass formers; intense motor action promotes reconfiguration. The fact that our model assuming a negative motor susceptibility predicts the latter suggests that on average the motorized processes in living cells do resist the imposed mechanical load. Our calculations also identify a spinodal point where simultaneously the mismatch penalty vanishes and the mechanical stability of amorphous packing disappears., Comment: 23 pages, 12 figures

The remarkable strength of glasses is examined using the random first order transition theory of the glass transition. The theory predicts that strength depends on elastic modulus but also on the configurational energy frozen in when the glass is prepared. The stress catalysis of cooperative rearrangements of the type responsible for the supercooled liquid's high viscosity account quantitatively for the measured strength of a range of metallic glasses, silica and a polymer glass., Comment: 22 pages, 6 figures

Many transcription factors bind to DNA with a remarkable lack of specificity, so that regulatory binding sites compete with an enormous number of non-regulatory 'decoy' sites. For an auto-regulated gene, we show decoy sites decrease noise in the number of unbound proteins to a Poisson limit that results from binding and unbinding. This noise buffering is optimized for a given protein concentration when decoys have a 1/2 probability of being occupied. Decoys linearly increase the time to approach steady state and exponentially increase the time to switch epigenetically between bistable states., Comment: 8 pages, 4 figures

Actomyosin networks are major structural components of the cell. They provide mechanical integrity and allow dynamic remodeling of eukaryotic cells, self-organizing into the diverse patterns essential for development. We provide a theoretical framework to investigate the intricate interplay between local force generation, network connectivity and collective action of molecular motors. This framework is capable of accommodating both regular and heterogeneous pattern formation, arrested coarsening and macroscopic contraction in a unified manner. We model the actomyosin system as a motorized cat's cradle consisting of a crosslinked network of nonlinear elastic filaments subjected to spatially anti-correlated motor kicks acting on motorized (fibril) crosslinks. The phase diagram suggests there can be arrested phase separation which provides a natural explanation for the aggregation and coalescence of actomyosin condensates. Simulation studies confirm the theoretical picture that a nonequilibrium many-body system driven by correlated motor kicks can behave as if it were at an effective equilibrium, but with modified interactions that account for the correlation of the motor driven motions of the actively bonded nodes. Regular aster patterns are observed both in Brownian dynamics simulations at effective equilibrium and in the complete stochastic simulations. The results show that large-scale contraction requires correlated kicking., Comment: 38 pages, 13 figures

Contractile forces are essential for many developmental processes involving cell shape change and tissue deformation. Recent experiments on reconstituted actomyosin networks, the major component of the contractile machinery, have shown that active contractility occurs above a threshold motor concentration and within a window of crosslink concentration. We present a microscopic dynamic model that incorporates two essential aspects of actomyosin self-organization: the asymmetric load response of individual actin filaments and the correlated motor-driven events mimicking myosin-induced filament sliding. Using computer simulations we examine how the concentration and susceptibility of motors contribute to their collective behavior and interplay with the network connectivity to regulate macroscopic contractility. Our model is shown to capture the formation and dynamics of contractile structures and agree with the observed dependence of active contractility on microscopic parameters including the contractility onset. Cooperative action of load-resisting motors in a force-percolating structure integrates local contraction/buckling events into a global contractile state via an active coarsening process, in contrast to the flow transition driven by uncorrelated kicks of susceptible motors., Comment: 15 pages, 4 main figures, 4 supplementary figures

The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, crosslink concentration, filament length and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density., Comment: 17 pages, 18 figures

Spontaneous directed motion, a hallmark of cell biology, is unusual in classical statistical physics. Here we study, using both numerical and analytical methods, organized motion in models of the cytoskeleton in which constituents are driven by energy-consuming motors. While systems driven by small-step motors are described by an effective temperature and are thus quiescent, at higher order in step size, both homogeneous and inhomogeneous, flowing and oscillating behavior emerges. Motors that respond with a negative susceptibility to imposed forces lead to an apparent negative-temperature system in which beautiful structures form resembling the asters seen in cell division., Comment: 17 pages, 5 figures (2 supplementary figures)

A systematic expansion of the many-body master equation for active matter, in which motors power configurational changes as in the cytoskeleton, is shown to yield a description of the steady state and responses in terms of an effective temperature. The effective temperature depends on the susceptibility of the motors and a Peclet number which measures their strength relative to thermal Brownian diffusion. The analytic prediction is shown to agree with previous numerical simulations and experiments. The mapping also establishes a description of aging in active matter that is also kinetically jammed., Comment: 2 figures