Related papers: Single-Trajectory Bayesian Modeling Reveals Multi-…
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…
We study a minimal lattice model which describes bidirectional transport of "particles" driven along a one dimensional track, as is observed in microtubule based, motor protein driven bidirectional transport of cargo vesicles, lipid bodies…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate…
Transporting between arbitrary distributions is a fundamental goal in generative modeling. Recently proposed diffusion bridge models provide a potential solution, but they rely on a joint distribution that is difficult to obtain in…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
With intelligent room-side sensing and service robots widely deployed, human motion prediction (HMP) is essential for safe, proactive assistance. However, many existing HMP methods either produce a single, deterministic forecast that…
A novel probabilistic framework for modelling anomalous diffusion is presented. The resulting process is Markovian, non-homogeneous, non-stationary, non-ergodic, and state-dependent. The fundamental law governing this process is driven by…
The Mean Square Displacement is a central tool in the analysis of Single Particle Tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time-averages on single particle…
Conformational changes drive protein function, including catalysis, allostery, and signaling. X-ray diffuse scattering from protein crystals has frequently been cited as a probe of these correlated motions, with significant potential to…
Protein complexes involved in DNA mismatch repair appear to diffuse along dsDNA in order to locate a hemimethylated incision site via a dissociative mechanism. Here, we study the probability that these complexes locate a given target site…
Witnessing and tracking topological phase transitions induced by interactions with the environment is a crucial challenge. Among the various experimental approaches to detect topological properties, the Mean Chiral Displacement (MCD) has…
Periodic reversals of the direction of motion in systems of self-propelled rod shaped bacteria enable them to effectively resolve traffic jams formed during swarming and maximize their swarming rate. In this paper, a connection is found…
A prime example of non-equilibrium or active environment is a biological cell. In order to understand in-vivo functioning of biomolecules such as proteins, chromatins, a description beyond equilibrium is absolutely necessary. In this…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
Masked diffusion models (MDMs) generate discrete sequences by iterative denoising under an absorbing masking process. In standard masked diffusion, if a token remains masked after a reverse update, the model discards its clean-state…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
The diffusion of molecules (penetrants) of variable size, shape, and chemistry through dense crosslinked polymer networks is a fundamental scientific problem that is broadly relevant in materials, polymer, physical and biological chemistry.…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…