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Cell stiffness is a key determinant of how cells deform, migrate, and adapt to mechanically restrictive environments, yet existing single-cell stiffness assays remain difficult to combine with molecular analysis and downstream functional…
Single-cell data reveal the presence of biological stochasticity between cells of identical genome and environment, in particular highlighting the transcriptional bursting phenomenon. To account for this property, gene expression may be…
Constant potential method molecular dynamics simulation (CPM MD) enables the accurate modelling of atomistic electrode charges when studying the electrode-electrolyte interface at the nanoscale. Here we extend the theoretical framework of…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
We develop a robust coarse-grained model for single and double stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes…
Smoothed Particle Hydrodynamics (SPH) methods are advantageous in simulations of fluids in domains with free boundary. Special SPH methods have also been developed to simulate solids. However, there are situations where the matter behaves…
We explore the roles of electronic band structure and Coulomb interactions in solid-state HHG by studying the optical response of linear atomic chains and carbon nanotubes to intense ultrashort pulses. Specifically, we simulate electron…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
Increased ability to predict protein structures is moving research focus towards understanding protein dynamics. A promising approach is to represent protein dynamics through networks and take advantage of well-developed methods from…
DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation,…
We have managed to correlate the stability constants of complex formation, which can be registered in equilibrium state, to the dynamic characteristic of the complex lifetime. Thus, the principal concept of molecular biophysics regarding…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
In fluid dynamical simulations in astrophysics, large deformations are common and surface tracking is sometimes necessary. Smoothed Particle Hydrodynamics (SPH) method has been used in many of such simulations. Recently, however, it has…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of…
Biological systems achieve adaptive mechanical responses through reaction-diffusion processes that couple chemical wave propagation to structural transitions. Although synthetic hydrogels with enzymatic reactions offer a platform for…
Semiflexible polymers form central structures in biological material. Modeling approaches usually neglect influences of polymer-specific molecular features aiming to describe semiflexible polymers universally. Here, we investigate the…
Capturing the dynamics of active particles, i.e., small self-propelled agents that both deform and are deformed by a fluid in which they move is a formidable problem as it requires coupling fine scale hydrodynamics with large scale…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…