Related papers: Optimal flexibility for conformational transitions…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Within the germinal center in follicles, B-cells proliferate, mutate and differentiate, while being submitted to a powerful selection~: a micro-evolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted…
Structure-based molecular ML (SBML) models can be highly sensitive to input geometries and give predictions with large variance. We present an approach to mitigate the challenge of selecting conformations for such models by generating…
Unlike conventional mechanisms, compliant mechanisms produce the desired deformations by exploiting elastic strain and do not need, therefore, moving parts. The number of degrees of freedom of a conventional mechanism, also called mobility,…
It has become clear in recent years that the simple uniform wormlike chain model needs to be modified in order to account for more complex behavior which has been observed experimentally in some important biopolymers. For example, the large…
Many-body localization (MBL) is a novel prototype of ergodicity breaking due to the emergence of local integrals of motion (LIOMs) in a disordered interacting quantum system. To better understand the role played by the existence of such…
Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…
To understand the mechanism of TATA-box conformational transformations we model structure mobility and find the types of conformational excitations of DNA macromolecule in heteronomous conformation. We have constructed the two-component…
The mode-coupling theory for ideal glass transitions in simple systems is generalized to a theory for the glassy dynamics of molecular liquids using the density fluctuations of the sites of the molecule's constituent atoms as the basic…
Biomolecular conformational transitions are usually modeled as barrier crossings in a free energy landscape. The transition paths connect two local free energy minima and transition path times (TPT) are the actual durations of the crossing…
We study a simplified two-dimensional model for a cubic-to-orthorhombic phase transition occuring in certain shape-memory-alloys. In the low temperature regime the linear theory of elasticity predicts various possible patterns of martensite…
In transfer learning, we wish to make inference about a target population when we have access to data both from the distribution itself, and from a different but related source distribution. We introduce a flexible framework for transfer…
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139…
Cells and organisms follow aligned structures in their environment, a process that can generate persistent migration paths. Kinetic transport equations are a popular modelling tool for describing biological movements at the mesoscopic…
We consider an isolated point defect embedded in a homogeneous crystalline solid. We show that, in the harmonic approximation, a periodic supercell approximation of the formation free energy as well as of the transition rate between two…
Mechanical metamaterials are periodic lattice structures with complex unit cell architectures that can achieve extraordinary mechanical properties beyond the capability of bulk materials. A new class of metamaterials is proposed, whose…
Cells are complex structures which require considerable amounts of organization via transport of large intracellular cargo. While passive diffusion is often sufficiently fast for the transport of smaller cargo, active transport is necessary…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
The interlayer couplings in commensurate and incommensurate bilayer structures of transition metal dichalcogenides are investigated with perturbative treatment. The interlayer coupling in \pm K valleys can be decomposed into a series of…
Cancer cell migration between different body parts is the driving force behind cancer metastasis, which is the main cause of mortality of patients. Migration of cancer cells often proceeds by penetration through narrow cavities in locally…