Related papers: Diagnosing Heterogeneous Dynamics in Single Molecu…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
To understand the non-equilibrium relaxation dynamics of a liquid droplet on a switchable substrate the interplay of different length- and time-scales needs to be understood. We present a method to map the microscopic information, resulting…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
Using probabilistic approach, the transient dynamics of sparsely connected Hopfield neural networks is studied for arbitrary degree distributions. A recursive scheme is developed to determine the time evolution of overlap parameters. As…
Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in…
We present a novel, real-time algorithm to track the trajectory of each pedestrian in moderately dense crowded scenes. Our formulation is based on an adaptive particle-filtering scheme that uses a combination of various multi-agent…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
A Bayesian data assimilation scheme is formulated for advection-dominated or hyperbolic evolutionary problems, and observations. The method is referred to as the dynamic likelihood filter because it exploits the model physics to dynamically…
Cell migration is an indispensable physiological and pathological process for normal tissue development and cancer metastasis, which is greatly regulated by intracellular signal pathways and extracellular microenvironment (ECM). However,…
Temperature is a fundamental regulator of chemical and biochemical kinetics, yet capturing nonlinear thermal effects directly from experimental data remains a major challenge due to limited throughput and model flexibility. Recent advances…
With the advance of fluorescence imaging technologies, recently cell biologists are able to record the movement of protein vesicles within a living cell. Automatic tracking of the movements of these vesicles become key for qualitative…
We compute profile likelihoods for a stochastic model of diffusive transport motivated by experimental observations of heat conduction in layered skin tissues. This process is modelled as a random walk in a layered one-dimensional material,…
An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
Simulating percolation and critical phenomena of labelled species inside films composed of single-component linear homogeneous macromolecules using molecular Monte Carlo method in 3 dimensions, we study dependence of these conducting…
The dynamical heterogeneity in supercooled liquids measured by a molecular dynamics simulation has been quantified on the basis of the multifractal formalism. The singularity spectrum becomes broader as the glass transition is approached.…