arXiv subjects

J. N. Milstein

Publications and source records attributed to J. N. Milstein.

12 recordsLinked to original sources

arXiv2010

Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal motion of the DNA and other fluctuations of the cellular environment. We present single-molecule measurements of DNA loop formation and breakdown when an artificial fluctuating force, applied to mimic a fluctuating cellular environment, is imposed on the DNA. We show that loop formation is greatly enhanced in the presence of noise of only a fraction of $k_B T$, yet find that hypothetical regulatory schemes that employ mechanical tension in the DNA--as a sensitive switch to control transcription--can be surprisingly robust due to a fortuitous cancellation of noise effects.

q-bio.BM↗

arXiv2010

Femtonewton Forces Can Control Protein-Meditated DNA Looping

We show that minuscule entropic forces, on the order of 100 fN, can prevent the formation of DNA loops--a ubiquitous means of regulating the expression of genes. We observe a tenfold decrease in the rate of LacI-mediated DNA loop formation when a tension of 200 fN is applied to the substrate DNA, biasing the thermal fluctuations that drive loop formation and breakdown events. Conversely, once looped, the DNA-protein complex is insensitive to applied force. Our measurements are in excellent agreement with a simple polymer model of loop formation in DNA, and show that an anti-parallel topology is the preferred LacI-DNA loop conformation for a generic loop-forming construct.

q-bio.BM↗

arXiv2008

Neuronal Shot Noise and Brownian $1/f^2$ Behavior in the Local Field Potential

We demonstrate that human electrophysiological recordings of the local field potential (LFP) from intracranial electrodes, acquired from a variety of cerebral regions, show a ubiquitous $1/f^2$ scaling within the power spectrum. We develop a quantitative model that treats the generation of these fields in an analogous way to that of electronic shot noise, and use this model to specifically address the cause of this $1/f^2$ Brownian noise. The model gives way to two analytically tractable solutions, both displaying Brownian noise: 1) uncorrelated cells that display sharp initial activity, whose extracellular fields slowly decay and 2) rapidly firing, temporally correlated cells that generate UP-DOWN states.

q-bio.NC↗

arXiv2007

Dynamic Moment Analysis of the Extracellular Electric Field of a Biologically Realistic Spiking Neuron

Based upon the membrane currents generated by an action potential in a biologically realistic model of a pyramidal, hippocampal cell within rat CA1, we perform a moment expansion of the extracellular field potential. We decompose the potential into both inverse and classical moments and show that this method is a rapid and efficient way to calculate the extracellular field both near and far from the cell body. The action potential gives rise to a large quadrupole moment that contributes to the extracellular field up to distances of almost 1 cm. This method will serve as a starting point in connecting the microscopic generation of electric fields at the level of neurons to macroscopic observables such as the local field potential.

q-bio.NC↗

arXiv2007

Classical field techniques for condensates in one-dimensional rings at finite temperatures

For a condensate in a one-dimensional ring geometry, we compare the thermodynamic properties of three conceptually different classical field techniques: stochastic dynamics, microcanonical molecular dynamics, and the classical field method. Starting from non-equilibrium initial conditions, all three methods approach steady states whose distribution and correlation functions are in excellent agreement with an exact evaluation of the partition function in the high-temperature limit. Our study helps to establish these various classical field techniques as powerful non-perturbative tools for systems at finite temperatures.

cond-mat.other↗

arXiv2005

Superfluidity and binary-correlations within clusters of fermions

We propose a method for simulating the behaviour of small clusters of particles that explicitly accounts for all mean-field and binary-correlation effects. Our approach leads to a set of variational equations that can be used to study both the dynamics and thermodynamics of these clusters. As an illustration of this method, we explore the BCS-BEC crossover in the simple model of four fermions, interacting with finite-range potentials, in a harmonic potential. We find, in the crossover regime, that the particles prefer to occupy two distinct pair states as opposed to the one assumed by BCS theory.

cond-mat.other↗

arXiv2004

The Nature of Superfluidity in Ultracold Fermi Gases Near Feshbach Resonances

We study the superfluid state of atomic Fermi gases using a BCS-BEC crossover theory. Our approach emphasizes non-condensed fermion pairs which strongly hybridize with their (Feshbach-induced) molecular boson counterparts. These pairs lead to pseudogap effects above $T_c$ and non-BCS characteristics below. We discuss how these effects influence the experimental signatures of superfluidity.

cond-mat.soft↗

arXiv2003

Resonant formation of strongly correlated paired states in rotating Bose gases

We propose increasing the fractional quantum Hall gap of a rapidly rotating Bose gas by increasing the interatomic interactions via a Feshbach resonance. The generation of molecules by the resonance causes pair correlations to grow throughout the system effecting the ground state. By an extension of the usual Chern-Simons theory, built of composite atoms and molecules, we are able to account for these resonance effects. We find that the resulting ground state evolves from a Laughlin wavefunction to a unique paired wavefunction as one approaches the resonance.

cond-mat.soft↗

arXiv2003

Feshbach resonances and collapsing Bose-Einstein condensates

We investigate the quantum state of burst atoms seen in the recent Rb-85 experiments at JILA. We show that the presence of a resonance scattering state can lead to a pairing instability generating an outflow of atoms with energy comparable to that observed. A resonance effective field theory is used to study this dynamical process in an inhomogeneous system with spherical symmetry.

cond-mat.soft↗

arXiv2002

Resonance theory of the crossover from Bardeen-Cooper-Schrieffer superfluidity to Bose-Einstein condensation in a dilute Fermi gas

We present a description of the behavior of a superfluid gas of fermions in the presence of a Feshbach resonance over the complete range of magnetic field detunings. Starting from a resonance Hamiltonian, we exploit a functional method to describe the continuous behavior from Bardeen-Cooper-Schrieffer to Bose-Einstein condensation type superfluidity. Our results show an ability for a resonance system to exhibit a high critical temperature comparable to the Fermi temperature. The results are derived in a manner that is shown to be consistent with the underlying microscopic scattering physics.

cond-mat.soft↗

arXiv2001

Resonance Superfluidity: Renormalization of Resonance Scattering Theory

We derive a theory of superfluidity for a dilute Fermi gas that is valid when scattering resonances are present. The treatment of a resonance in many-body atomic physics requires a novel mean-field approach starting from an unconventional microscopic Hamiltonian. The mean-field equations incorporate the microscopic scattering physics, and the solutions to these equations reproduce the energy-dependent scattering properties. This theory describes the high-$T_c$ behavior of the system, and predicts a value of $T_c$ which is a significant fraction of the Fermi temperature. It is shown that this novel mean-field approach does not break down for typical experimental circumstances, even at detunings close to resonance. As an example of the application of our theory we investigate the feasibility for achieving superfluidity in an ultracold gas of fermionic $^6$Li.

cond-mat.soft↗

arXiv2001

Signatures of resonance superfluidity in a quantum Fermi gas

In this letter, we predict a direct and observable signature of the superfluid phase in a quantum Fermi gas, in a temperature regime already accessible in current experiments. We apply the theory of resonance superfluidity to a gas confined in a harmonic potential and demonstrate that a significant increase in density will be observed in the vicinity of the trap center.

cond-mat↗