Related papers: Exploring the Free Energy Landscape: From Dynamics…
The long-standing, dominant approach to robotic obstacle negotiation relies on mapping environmental geometry to avoid obstacles. However, this approach does not allow for traversal of cluttered obstacles, hindering applications such as…
A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local…
Cancer is a systemic heterogeneous disease involving complex molecular networks. Tumor formation involves epithelial-mesenchymal transition (EMT), which promotes both metastasis and plasticity of cancer cells. Recent experiments proposed…
Advancements in artificial intelligence call for a deeper understanding of the fundamental mechanisms underlying deep learning. In this work, we propose a theoretical framework to analyze learning dynamics through the lens of dynamical…
Many complex structures and stochastic patterns emerge from simple kinetic rules and local interactions, and are governed by scale invariance properties in combination with effects of the global geometry. We consider systems that can be…
An efficient numerical framework is presented for modeling viscoelasticity and permanent set of polymers. It is based on the hereditary integral form of transient network theory, in which polymer chains belong to distinct networks each with…
In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore,…
Curvature-sensing and curvature-remodeling proteins are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can…
Models of biochemical networks are usually presented as connected graphs where vertices indicate proteins and edges are drawn to indicate activation or inhibition relationships. These diagrams are useful for drawing qualitative conclusions…
We study the dissociative adsorption of methane at the surface of graphene. Free energy profiles, which include activation energies for different steps of the reaction, are computed from constrained ab initio molecular dynamics. At 300 K,…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
Complex energy landscapes often arise in biological systems, e.g. for protein folding, biochemical reactions or intracellular transport processes. Their physical effects are often reflected in the first-passage times arising from these…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
We calculate the statistical properties of the energy landscape of a minimal model for strong network-forming liquids. Dynamics and thermodynamic properties of this model can be computed with arbitrary precision even at low temperatures. A…
The paper analyses stochastic systems describing reacting molecular systems with a combination of two types of state spaces, a finite-dimensional, and an infinite dimenional part. As a typical situation consider the interaction of larger…
Systems with many interacting stochastic constituents are fully characterized by their free energy. Computing this quantity is therefore the objective of various approaches, notably perturbative expansions, which are applied in problems…
We study a family of networks of autocatalytic reactions, which we call hyperchains, that are a generalization of hypercycles. Hyperchains, and the associated dynamical system called replicator equations, are a possible mechanism for…
Molecular transitions -- such as protein folding, allostery, and membrane transport -- are central to biology yet remain notoriously difficult to simulate. Their intrinsic rarity pushes them beyond reach of standard molecular dynamics,…
Rare transitions between long-lived stable states are often analyzed in terms of free energy landscapes computed as functions of a few collective variables. Here, using transitions between geometric phases as example, we demonstrate that…