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Stochastic models for pore collapse in granular materials are developed. First, a general fluctuating stress-strain relation for a plastic flow rule is derived. The fluctuations account for non-associativity in plastic deformations…
In battery modeling, the electrode is discretized at the macroscopic scale with a single representative particle in each volume. This lacks the accurate physics to describe interparticle interactions in electrodes. To remedy this, we…
The functions of most genetic circuits require sufficient degrees of cooperativity in the circuit components. While mechanisms of cooperativity have been studied most extensively in the context of transcriptional initiation control,…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Background: Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix and intracellular actions. By…
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various…
Disordered fibrous matrices, formed by the random assembly of fibers, provide the structural framework for many biological systems and biomaterials. Applied deformation modifies the alignment and stress states of constituent fibers, tuning…
Using molecular dynamics computer simulations we investigate the aging dynamics of a gel. We start from a fractal structure generated by the DLCA-DEF algorithm, onto which we then impose an interaction potential consisting of a short-range…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
In this paper we develop a lattice-based computational model focused on bone resorption by osteoclasts in a single cortical basic multicellular unit (BMU). Our model takes into account the interaction of osteoclasts with the bone matrix,…
Molecular diffusion measurements are widely used to probe microstructure in materials and living organisms noninvasively. The precise relation of diffusion metrics to microstructure remains a major challenge: In complex samples, it is often…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Filamentous bio-materials such as fibrin or collagen networks exhibit an enormous stiffening of their elastic moduli upon large deformations. This pronounced nonlinear behavior stems from a significant separation between the stiffnesses…
Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains…
Many biological tissues feature a heterogeneous network of fibers whose tensile and bending rigidity contribute substantially to these tissues' elastic properties. Rigidity percolation has emerged as a important paradigm for relating these…
Essential life processes take place across multiple space and time scales in living organisms but understanding their mechanistic interactions remains an ongoing challenge. Advanced multiscale modeling techniques are providing new…
It is well-known that the architecture of macromolecules plays an important role in the hydrodynamics and viscosity of its semi-diluted solutions. However, the systematic study of the rheology of macromolecules with complex topology, such…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
The aim of this work is to develop a 3D finite elements model to study the nanomechanical behaviour of mineralized collagen microfibrils, which consists of three phases, (i) collagen phase formed by five tropocollagen (TC) molecules linked…
Uncovering microstructure evolution mechanisms that accompany the long-term operation of solid oxide fuel cells is a fundamental challenge in designing a more durable energy system for the future. To date, the study of fuel cell stack…