Related papers: Stochastic Dynamics of Bionanosystems: Multiscale …
We propose a mathematical kinetic framework to investigate interactions between tumor cells and the immune system, focusing on the spatial dynamics of tumor progression and immune responses. We develop two kinetic models: one describes a…
A generalization of the microcanonical ensemble suggests a simple strategy for the simulation of first order phase transitions. At variance with flat-histogram methods, there is no iterative parameters optimization, nor long waits for…
Dynamical maps describe general transformations of the state of a physical system, and their iteration can be interpreted as generating a discrete time evolution. Prime examples include classical nonlinear systems undergoing transitions to…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
Interacting spin-boson models encompass a large class of physical systems, spanning models with a single spin interacting with a bosonic bath -- a paradigm of quantum impurity problems -- to models with many spins interacting with a cavity…
A general framework to describe a vast majority of biology-inspired systems is to model them as stochastic processes in which multiple couplings are in play at the same time. Molecular motors, chemical reaction networks, catalytic enzymes,…
Stochastic hydrodynamics is a central tool in the study of first order phase transitions at a fundamental level. Combined with sophisticated free energy models, e.g. as developed in classical Density Functional Theory, complex processes…
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent…
The multi-level method for discrete state systems, first introduced by Anderson and Higham [Multiscale Model. Simul. 10:146--179, 2012], is a highly efficient simulation technique that can be used to elucidate statistical characteristics of…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
Bacteria generally live in complicated structures called biofilms, consisting of communicating bacterial colonies and extracellular polymeric substance (EPS). Since biofilms are related to detrimental effects such as infection or antibiotic…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
A general formulation of stochastic thermodynamics is presented for open systems exchanging energy and particles with multiple reservoirs. By introducing a partition in terms of "macrostates" (e.g. sets of "microstates"), the consequence on…
We provide a stochastic thermodynamic description across scales for $N$ identical units with all-to-all interactions that are driven away from equilibrium by different reservoirs and external forces. We start at the microscopic level with…
Currently, identification of crystallization pathways in polymers is being carried out using molecular simulation-based data on a preset cut-off point on a single order parameter (OP) to define nucleated or crystallized regions. Aside from…
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
We develop a comprehensive theoretical biophysics model grounded in a path integral perspective and an m-sectorial open-system framework, to describe complex, damped viral phonon dynamics in resource limited and noise driven environments.…