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We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves…
We investigate quantum transport characteristics of a ladder model, which effectively mimics the topology of a double-stranded DNA molecule. We consider the interaction of tunneling charges with a selected internal vibrational degree of…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
A distinguishing feature of active particles is the nature of the non-equilibrium noise driving their dynamics. Control of these noise properties is, therefore, of both fundamental and applied interest. We demonstrate emergent tuning of the…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
Single-filament tracing has been a valuable tool to directly determine geometrical and mechanical properties of entangled polymer networks. However, systematically verifying how the stiffness of the tracer filament or its molecular…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
Ionization profile monitors (IPMs) are widely used in particle accelerators for fast evaluation of parameters of high energy beams. Due to the space-charge effects and several other physical reasons, as well as due to instrumental effects,…
Particle-wall interactions play a crucially important role in various applications such as microfluidic devices for cell sorting, particle separation, entire class of hydrodynamic filtration and its derivatives, etc. Yet, accurate…
The motivation for this study came from the task of analysing the kinetic behavior of single molecules in a living cell based on Single Molecule Localization Microscopy. Given measurements of both the motion of clusters and molecules, the…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
We study the tagged particle dynamics in a harmonic chain of direction reversing active Brownian particles, with spring constant $k$, rotation diffusion coefficient $D_{\text{r}}$, and directional reversal rate $\gamma$. We exactly compute…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
We propose a new method for absolute momentum calibration of magnetic spectrometers used in nuclear physics, using the time-of-flight (TOF), differences of pairs of particles with different masses. In cases where the flight path is not…
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
We construct a theoretical model for the dynamics of a microscale colloidal particle, modeled as an interval, moving horizontally on a DNA-coated surface, modelled as a line coated with springs that can stick to the interval. Averaging over…
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the…
Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) which converges back to a Brownian motion with reduced diffusion coefficient at long times, after the anomalous…
Dielectrophoretic trapping of six different DNA fragments, sizes varying from the 27 to 8416 bp, has been studied using confocal microscopy. The effect of the DNA length and the size of the constriction between nanoscale fingertip…