Related papers: Minimum energy paths for conformational changes of…
We propose a scheme to perform the variational principle directly on the coherent pair condensate (VDPC). The result is equivalent to that of the so-called variation after particle-number projection, but now the particle number is always…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
Nanoindentation of viral capsids provides an efficient tool in order to probe their elastic properties. We investigate in the present work the various sources of stiffness heterogeneity as observed in Atomic Force Microscopy (AFM)…
In this paper, we propose a novel minimal physical model to elucidate the long-term stochastic variability of blazars. The model is built on the realistic background of magnetized plasma jets dissipating energy through a turbulent cascade…
We present a time dependent variational method to learn the mechanisms of equilibrium reactive processes and efficiently evaluate their rates within a transition path ensemble. This approach builds off variational path sampling methodology…
We conjecture that certain patterns (scars), theoretically and numerically predicted to be formed by electrons arranged on a sphere to minimize the repulsive Coulomb potential (the Thomson problem) and experimentally found in spherical…
Elucidating the interplay of defect and stress at the microscopic level is a fundamental physical problem that has strong connection with materials science. Here, based on the two-dimensional crystal model, we show that the instability mode…
Virus binding to a surface results at least locally, at the contact area, in stress and potential structural perturbation of the virus cage. Here we address the question of the role of substrate-induced deformation in the overall virus…
We prove the existence of a phase transition in dimension $d>1$ in a continuum particle system interacting with a pair potential containing a modified attractive Kac potential of range $\gamma^{-1}$, with $\gamma>0$. This transition is…
A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, {\it rotors}, and…
Trapping macromolecules is impoartant for the study of their conformations, interactions, dynamics and kinetic processes. Here, we develop a variational approach which self-consistently introduces a mean force that controls the…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
Hierarchical (first-order) structured deformations are studied from the variational point of view. The main contributions of the present research are the first steps, at the theoretical level, to establish a variational framework to…
Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…
A variational method is used to derive a self-consistent macro-particle model for relativistic electromagnetic kinetic plasma simulations. Extending earlier work [E. G. Evstatiev and B. A. Shadwick, J. Comput. Phys., vol. 245, pp. 376-398,…
It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures,…
We investigate the dynamics of a single, overdamped colloidal particle, which is driven by a constant force through a one-dimensional periodic potential. We focus on systems with large barrier heights where the lowest-order cumulants of the…
Recent high resolution structures for viral capsids with 12, 32 and 72 subunits ($T1$, $T3$ and $T7$ viruses) have confirmed theoretical predictions of an icosadeltahedral structure with 12 subunits having five nearest neighbors (pentamers)…
The present work address the problem of energy shaping for stochastic port-Hamiltonian system. Energy shaping is a powerful technique that allows to systematically find feedback law to shape the Hamiltonian of a controlled system so that,…
We develop equilibrium and kinetic theories that describe the assembly of viral capsid proteins on a charged central core, as seen in recent experiments in which brome mosaic virus (BMV) capsids assemble around nanoparticles functionalized…