Related papers: Measuring ligand-receptor binding kinetics and dyn…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
High-throughput screening using cell images is an efficient method for screening new candidates for pharmaceutical drugs. To complete the screening process, it is essential to have an efficient process for analyzing cell images. This paper…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
The results of kinetic simulations of magnetic reconnection in Harris current sheets are analyzed. A range of guide fields is considered to study reconnection in plasmas characterized by different $\beta$ values, $\beta > m_e/m_i$. Both an…
The advent in recent years of highly parallelized microfluidic chemical reaction systems necessitates an understanding of all fluid dynamic time scales including the often neglected millisecond time scale of the inertia of the liquid. We…
Biological tissue integrity is actively maintained by cells. It is essential to comprehend how cells accomplish this in order to stage tissue diseases. However, addressing the complexity of a cell's system of interrelated mechanisms poses a…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Particle-in-Cell (PIC) method is a powerful plasma simulation tool for investigating high-intensity femtosecond laser-matter interaction. However, its simulation capability at high-density plasmas around the Fermi temperature is considered…
An optical kink is a shock-wave-like field structure which can appear in a resonant two-level medium as a result of the nonlinear process of self-steepening. We numerically simulate this process using an adiabatically switching waveform as…
We report the cell biological applications of a recently developed multiphoton fluorescence lifetime imaging microscopy system using a streak camera (StreakFLIM). The system was calibrated with standard fluorophore specimens and was shown…
Despite a large body of work, the exact molecular details underlying ion-selectivity and transport in the potassium channel have not been fully laid to rest. One major reason has been the lack of experimental methods that can probe these…
Time-resolved mapping of lattice dynamics in real- and momentum-space is essential to understand better several ubiquitous phenomena such as heat transport, displacive phase transition, thermal conductivity, and many more. In this regard,…
Protein mobility is conventionally analyzed in terms of an effective diffusion. Yet, this description often fails to properly distinguish and evaluate the physical parameters (such as the membrane friction) and the biochemical interactions…
We describe a systematic development of kinetic entropy as a diagnostic in fully kinetic particle-in-cell (PIC) simulations and use it to interpret plasma physics processes in heliospheric, planetary, and astrophysical systems. First, we…
This paper develops a molecular integrated sensing and communication (ISAC) framework that exploits the same molecular observations for physical-parameter sensing and data detection. As a representative instantiation, we consider a…
Reliably distinguishing between cells based on minute differences in receptor density is crucial for cell-cell or virus-cell recognition, the initiation of signal transduction and selective targeting in directed drug delivery. Such sharp…
We perform extensive 2D Particle-In-Cell (PIC) electromagnetic simulations of low pressure Inductively Coupled Plasma (ICP) discharges with various coil current and driving frequencies. Our simulations show that in low-frequency cases,…
Understanding the binding dynamics of liquid molecules is of fundamental importance in physical and life sciences. However, nanoscale fast dynamics pose great challenges for experimental characterization. Conventionally, the binding…
Cells continuously probe their environment with membrane receptors, achieving subsecond adaptation of their behaviour [1-3]. Recently, several receptors, including cadherins, were found to bind ligands with a lifetime of order of one…
Current methods for investigation of receptor - ligand interactions in drug discovery are based on three-dimensional complementarity of receptor and ligand surfaces, and they include pharmacophore modelling, QSAR, molecular docking etc.…