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In order to treat low-energy heavy-ion reactions, we make an extension of quantum molecular dynamics method. A phenomenological Pauli potential is introduced into effective interactions to approximate the nature of the Fermion many-body…
A rigorous limit procedure is presented which links nonlocal models involving adhesion or nonlocal chemotaxis to their local counterparts featuring haptotaxis and classical chemotaxis, respectively. It relies on a novel reformulation of the…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
This work presents a novel diffusion based dual-phase molecular communication system where the source leverages multiple cooperating nanomachines to improve the end-to-end reliability of communication. The Neyman-Pearson Likelihood Ratio…
We investigate the dynamics of a nonlinear system modeling tumor growth with drug application. The tumor is viewed as a mixture consisting of proliferating, quiescent and dead cells as well as a nutrient in the presence of a drug. The…
Vitrimers are polymer networks that can undergo bond exchange reactions. They dynamically rearrange their structures while maintaining their overall integrity, thus resulting in unique properties such as self-healing, reprocessability,…
The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…
Phenotype-based screening has attracted much attention for identifying cell-active compounds. Transcriptional and proteomic profiles of cell population or single cells are informative phenotypic measures of cellular responses to…
Research on conjugated polymers for thermoelectric applications has made tremendous progress in recent years, which is accompanied by surging interest in molecular doping as a means to achieve the high electrical conductivities that are…
Autologous chemotaxis, in which cells secrete and detect molecules to determine the direction of fluid flow, is thwarted at high cell density because molecules from other cells interfere with a given cell's signal. Using a minimal model of…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
Hydrogels are crosslinked polymer networks with high water content, widely employed in biomedical applications such as drug delivery, tissue engineering, and regenerative medicine. Injectable, depot-forming hydrogels enable sustained…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines…
Chemotaxis systems play a crucial role in modeling the dynamics of bacterial and cellular behaviors, including propagation, aggregation, and pattern formation, all under the influence of chemical signals. One notable characteristic of these…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Cancer is one of the most common diseases worldwide, posing a serious threat to human health and leading to the deaths of a large number of people. It was observed during the drug administration in chemotherapy that immune cells, cancer…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…