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Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular…
Fluorescence spectroscopy is an image correlation technique to analyze and characterize the molecular dynamics from a sequence of fluorescence images. Many image correlation techniques have been developed for different applications [1]. But…
Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it…
Airborne pathogen transmission mechanisms play a key role in the spread of infectious diseases such as COVID-19. In this work, we propose a computational fluid dynamics (CFD) approach to model and statistically characterize airborne…
To illustrate the power of the biophysical approach in solving important problems in life science, I present here one of our current research projects as an example. We have developed special biophotonic techniques to study the dynamic…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Single particle diffraction imaging experiments at free-electron lasers (FEL) have a great potential for structure determination of reproducible biological specimens that can not be crystallized. One of the challenges in processing the data…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
Diffusion Monte Carlo (DMC) based on fixed-node approximation has enjoyed significant developments in the past decades and become one of the go-to methods when accurate ground state energy of molecules and materials is needed. The remaining…
We study dynamics of a probe molecule, driven by an external constant force in a liquid monolayer on top of solid surface. In terms of a microscopic, mean-field-type approach, we calculate the terminal velocity of the probe molecule. This…
Diffusion processes in biological membranes are of interest to understand the macromolecular organisation and function of several molecules. Fluorescence Recovery After Photobleaching (FRAP) has been widely used as a method to analyse this…
Single molecule fluorescence tracking provides information at nm-scale and ms-temporal resolution about the dynamics and interaction of individual molecules in a biological environment. While the dynamic behavior of isolated molecules can…
The analysis of diffusion processes in real-world propagation scenarios often involves estimating variables that are not directly observed. These hidden variables include parental relationships, the strengths of connections between nodes,…
Heterogeneous diffusion processes occur in many different fields such as transport in living cells or diffusion in porous media. A characterization of the transport parameters of such processes can be achieved by ensemble-based methods,…
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…
Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT…
A constructive approach to theory of diffusion processes is proposed, which is based on application of both the symmetry analysis and method of modelling functions. An algorithm for construction of the modelling functions is suggested. This…
The motion of chemical bonds within molecules can be observed in real time, in the form of vibrational wavepackets prepared and interrogated through ultrafast nonlinear spectroscopy. Such nonlinear optical measurements are commonly…
Fluorescent molecules are versatile nanoscale emitters that enable detailed observations of biophysical processes with nanoscale resolution. Because they are well-approximated as electric dipoles, imaging systems can be designed to…