arXiv subjects

Peter G. Wolynes

Publications and source records attributed to Peter G. Wolynes.

At least 19 recordsLinked to original sources

arXiv2026

Statistics of Thermal Avalanches in Driven Amorphous Systems

Within the framework of the random first-order transition theory of glasses, we discuss the statistics of thermal avalanches, the large scale rearrangements in driven amorphous systems near their instability. Stringy excitations yield nonPoisson waiting time statistics. Embedding these statistics in a generalized Master equation captures the nonMarkovian, aging dynamics of avalanche clusters. We apply this framework to analyze nonequilibrium signatures of thermal avalanches, auto correlation functions and effective temperatures, under both quasi static shear and stochastic shaking protocols. We use full counting statistics to derive the complete distribution of both the avalanche magnitudes and avalanche counts, uncovering the intermediate time behavior.

cond-mat.dis-nn↗

arXiv2025

Quantum Simulation of Charge and Exciton Transfer in Multi-mode Models using Engineered Reservoirs

Quantum simulation offers a route to study open-system molecular dynamics in non-perturbative regimes by programming the interactions among electronic, vibrational, and environmental degrees of freedom on similar energy scales. Trapped-ion systems possess this capability, with their native spins, phonons, and tunable dissipation integrated within a single platform. Here, we demonstrate an open-system quantum simulation of charge and exciton transfer in a multi-mode linear vibronic coupling model. Employing tailored spin-phonon interactions alongside reservoir engineering techniques, we emulate a system with two dissipative vibrational modes coupled to donor and acceptor electronic sites and follow its non-equilibrium dynamics. We continuously tune the system from the charge transfer (CT) regime to the vibrationally assisted exciton transfer (VAET) regime by controlling the vibronic coupling strengths. We find that degenerate modes enhance CT and VAET rates at large energy gaps, while non-degenerate modes activate slow-mode pathways that reduce the energy-gap dependence, thus enlarging the window for efficient transfer. These results show that the presence of one additional vibration introduces interfering vibrationally assisted pathways and reshapes non-perturbative quantum excitation transfer. Our work establishes a scalable and hardware-efficient route to simulating chemically relevant, many-mode vibronic processes with engineered environments, guiding the design of next-generation organic photovoltaics and molecular electronics.

quant-ph↗

arXiv2025

Probing the Dark Energy in the Functional Protein Universe

We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the corresponding change to the apparent selection landscape of sequences over the evolutionary time scale. The difference between the physical folding free energies and the evolutionary free energies can be called a "Dark Energy". We analyse various protein sets and thereby show that Dark Energy is largely localized at functional sites, which are often energetically frustrated from the point of view of folding. Overall, we find that about 25% of the positions of the folded globular proteins display some significant Dark Energy. When a function relies on a free energy that can be thermodynamically quantified, such as a binding energy to a partner, the relationship of this physical free energy with Dark Energy can be used to define a Functional Selection Temperature. We show that selection for folding and binding functions bear similar weights in specific protein-protein interactions.

q-bio.BM↗

arXiv2025

Frustration In Physiology And Molecular Medicine

Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform these often amazing tasks, proteins must move and we must think of them as dynamic ensembles of three dimensional structures formed first by folding the polypeptide chains so as to minimize the conflicts between the interactions of their constituent amino acids. It is apparent however that, even when completely folded, not all conflicting interactions have been resolved so the structure remains "locally frustrated". Over the last decades it has become clearer that this local frustration is not just a random accident but plays an essential part of the inner workings of protein molecules. We will review here the physical origins of the frustration concept and review evidence that local frustration is important for protein physiology, protein-protein recognition, catalysis and allostery. Also, we highlight examples showing how alterations in the local frustration patterns can be linked to distinct pathologies. Finally we explore the extensions of the impact of frustration in higher order levels of organization of systems including gene regulatory networks and the neural networks of the brain.

q-bio.BM↗

arXiv2025

Motorized Chromosome Models of Mitosis

During mitosis, near-spherical chromosomes reconfigure into rod-like structures to ensure their accurate segregation to daughter cells. We explore here, the interplay between the nonequilibrium activity of molecular motors in determining the chromosomal organization in mitosis and its characteristic symmetry-breaking events. We present a hybrid motorized chromosome model that highlights the distinct roles of condensin I and II in shaping mitotic chromosomes. Guided by experimental observations, the simulations suggest that condensin II facilitates large-scale scaffold formation, while condensin I is paramount in local helical loop arrangement. Together, these two distinct grappling motors establish the hierarchical helical structure characteristic of mitotic chromosomes, which exhibit striking local and, sometimes global, chirality and contribute to the robust mechanical properties of mitotic chromosomes. Accompanying the emergence of rigidity, the model provides mechanisms of forming defects, including perversions and entanglements, and shows how these may be partially resolved through condensin activity and topoisomerase action. This framework bridges coarse-grained energy landscape models of chromosome dynamics and non-equilibrium molecular dynamics, advancing the understanding of chromosome organization during cell division and beyond.

physics.bio-ph↗

arXiv2025

Trapped-Ion Quantum Simulation of Electron Transfer Models with Tunable Dissipation

Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. By manipulating both the ground-state and optical qubits, we observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. 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.

quant-ph↗

arXiv2024

Reassessing the Exon-Foldon correspondence using Frustration Analysis

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.

q-bio.BM↗

arXiv2022

The Random First Order Transition Theory of Glasses in Real Space-Time: Instantons, Strings, Flames and Flows

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.

cond-mat.dis-nn↗

arXiv2022

Quantum Information Scrambling in Molecules

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.

physics.chem-ph↗

arXiv2018

Localization of Energetic Frustration in Proteins

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.

q-bio.BM↗

arXiv2017

Aging, jamming, and the limits of stability of amorphous solids

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.)

cond-mat.dis-nn↗

arXiv2017

Frustration, function and folding

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.

q-bio.BM↗

arXiv2015

Shape Transitions and Chiral Symmetry Breaking in the Energy Landscape of the Mitotic Chromosome

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.

physics.bio-ph↗

arXiv2015

On the hydrodynamics of swimming enzymes

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.

cond-mat.soft↗

arXiv2015

Dichotomous noise models of gene switches

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.

q-bio.MN↗

arXiv2014

Active patterning and asymmetric transport in a model actomyosin network

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.

cond-mat.soft↗

arXiv2014

Dynamical Heterogeneity in the Glassy State

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 $β$, 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.

cond-mat.stat-mech↗

arXiv2013

Frustration in Biomolecules

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.

q-bio.BM↗