Related papers: Variational Methods for Biomolecular Modeling
We introduce a simple spherical model whose structural properties are similar to the ones generated by models with directional interactions, by employing a binary mixture of large and small hard spheres, with a square-well attraction acting…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule…
We study the free energy and dynamics of a closed elastic filament (a one-dimensional curve in two dimensions) whose local internal state is specified by curvature, stretch, and a scalar density field representing, for example, the…
This paper investigates a variational approach to viscous flows with contact line dynamics based on energy-dissipation modeling. The corresponding model is reduced to a thin-film equation and its variational structure is also constructed…
The modeling of multi-energy systems (MES) is the basic task of analyzing energy systems integration. The variable energy efficiencies of the energy conversion and storage components in MES introduce nonlinearity to the model and thus…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years. The variational principle has opened the door for a nearly fully automated…
Many applications of porous media research involves high pressures and, correspondingly, exchange of thermal energy between the fluid and the matrix. While the system is relatively well understood for the case of non-moving porous media,…
The approach to the theory of many-particle interacting systems from a unified standpoint, based on the variational principle for free energy is reviewed. A systematic discussion is given of the approximate free energies of complex…
Soft interfaces formed by lipid membranes are fundamental to living cells, synthetic cells, and membrane-based soft materials. However, a quantitative framework linking molecular organization with nonlinear interfacial mechanics remains…
In this paper we consider a system of two coupled nonlinear diffusion--reaction partial differential equations (PDEs) which model the growth of biofilm and consumption of the nutrient. At the scale of interest the biofilm density is subject…
We consider sharp interface asymptotics for a phase field model of two phase near spherical biomembranes involving a coupling between the local mean curvature and the local composition proposed by the first and second authors. The model is…
We show how any system with morphological degrees of freedom and locally limited free energy will, under the constraints of the free energy principle, evolve toward a neuromorphic morphology that supports hierarchical computations in which…
Many physical situations are characterized by interfaces with a non trivial shape so that relevant geometric features, such as interfacial area, curvature or unit normal vector, can be used as main indicators of the topology of the…
Frictional properties of interfaces with dynamic chemical bonds have been the subject of intensive experimental investigation and modeling, as it provides important insights into the molecular origin of the empirical rate and state laws,…
Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
The structure of a network has a major effect on dynamical processes on that network. Many studies of the interplay between network structure and dynamics have focused on models of phenomena such as disease spread, opinion formation and…