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The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Collective cell motility is crucial to many biological processes including morphogenesis, wound healing, and cancer invasion. Recently, the biology and biophysics communities have begun to use the term cell jamming to describe the…
Unlike their model membrane counterparts, biological membranes are richly decorated with a heterogeneous assembly of membrane proteins. These proteins are so tightly packed that their excluded area interactions can alter the free energy…
Theoretical approaches are formulated to investigate the molecular mobility under various cooling rates of amorphous drugs. We describe the structural relaxation of a tagged molecule as a coupled process of cage-scale dynamics and…
The spatiotemporal coordination and regulation of cell proliferation is fundamental in many aspects of development and tissue maintenance. Cells have the ability to adapt their division rates in response to mechanical constraints, yet we do…
The concentration of intracellular calcium ion (Ca$^{2+}$) exhibits complex oscillations, including bursting and chaos, as observed experimentally. These dynamics are influenced by inherent fluctuations within cells, which serve as crucial…
Most of the intra-cellular events involved in the initiation and propagation phases of this process has now been identified astrocytes. The control of the spread of intracellular calcium signaling has been demonstrated to occur at several…
Understanding how neurons coordinate their activity is a fundamental question in neuroscience, with implications for learning, memory, and neurological disorders. Calcium imaging has emerged as a powerful method to observe large-scale…
Simple cubic structure with one atom in the unit cell found in compressed calcium is contrintuitive with regards to traditional view on tendency of transition to densely packed structures on the increase of pressure. To understand this…
Calcium batteries (CBs) are an attractive post-Li-ion technology, offering the appeal of Ca's natural abundance and high volumetric energy density. However, practical realization of CBs remains limited by the scarcity of positive electrode…
Compound-protein pairs dominate FDA-approved drug-target pairs and the prediction of compound-protein affinity and contact (CPAC) could help accelerate drug discovery. In this study we consider proteins as multi-modal data including 1D…
The coil-globule transition of hetero-polymer chains is studied here. By means of extensive Molecular Dynamics simulations, we show that the transition is directly linked to the complexity of the chain, which depends on the number of…
Cooperative action of molecular motors is essential for many cellular processes. One possible regulator of motor coordination is the elasticity-mediated crosstalk (EMC) coupling between myosin II motors whose origin is the tensile stress…
The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
Microtubules are an essential physical building block of cellular systems. They are organized using specific crosslinkers, motors, and influencers of nucleation and growth. With the addition of anti-parallel crosslinkers, microtubule…
Contractile forces exerted on the surrounding extracellular matrix (ECM) lead to the alignment and stretching of constituent fibers within the vicinity of cells. As a consequence, the matrix reorganizes to form thick bundles of aligned…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…