Confinement Effects on the Kinetics and Thermodynamics of Protein Dimerization

In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the interplay of these effects in the crowded cellular environment? We study dimerization of a model homodimer both when the mondimers are free or tethered to each other. We consider a structured environment: Two monomers first diffuse into a cavity of size $L$ and then fold and bind within the cavity. The folding and binding are simulated using molecular dynamics based on a simplified topology based model. The {\it confinement} in the cell is described by an effective molecular concentration $C \sim L^{-3}$. A two-state coupled folding and binding behavior is found. We show the maximal rate of dimerization occurred at an effective molecular concentration $C^{op}\simeq 1m$M which is a relevant cellular concentration. In contrast, for tethered chains the rate keeps at a plateau when $CC^{op}$. For both the free and tethered cases, the simulated variation of the rate of dimerization and thermodynamic stability with effective molecular concentration agrees well with experimental observations. In addition, a theoretical argument for the effects of confinement on dimerization is also made

The steady state quantum statistics of a non-Markovian atom laser

We present a fully quantum mechanical treatment of a single-mode atomic cavity with a pumping mechanism and an output coupling to a continuum of external modes. This system is a schematic description of an atom laser. In the dilute limit where atom-atom interactions are negligible, we have been able to solve this model without making the Born and Markov approximations. When coupling into free space, it is shown that for reasonable parameters there is a bound state which does not disperse, which means that there is no steady state. This bound state does not exist when gravity is included, and in that case the system reaches a steady state. We develop equations of motion for the two-time correlation in the presence of pumping and gravity in the output modes. We then calculate the steady-state output energy flux from the laser.Comment: 14 pages (twocloumn), 6 figure

Electrostatics of ions inside the nanopores and trans-membrane channels

A model of a finite cylindrical ion channel through a phospholipid membrane of width $L$ separating two electrolyte reservoirs is studied. Analytical solution of the Poisson equation is obtained for an arbitrary distribution of ions inside the trans-membrane pore. The solution is asymptotically exact in the limit of large ionic strength of electrolyte on the two sides of membrane. However, even for physiological concentrations of electrolyte, the electrostatic barrier sizes found using the theory are in excellent agreement with the numerical solution of the Poisson equation. The analytical solution is used to calculate the electrostatic potential energy profiles for pores containing charged protein residues. Availability of a semi-exact interionic potential should greatly facilitate the study of ionic transport through nanopores and ion channels

Effects of interatomic collisions on atom laser outcoupling

We present a computational approach to the outcoupling in a simple one-dimensional atom laser model, the objective being to circumvent mathematical difficulties arising from the breakdown of the Born and Markov approximations. The approach relies on the discretization of the continuum representing the reservoir of output modes, which allows the treatment of arbitrary forms of outcoupling as well as the incorporation of non-linear terms in the Hamiltonian, associated with interatomic collisions. By considering a single-mode trapped condensate, we study the influence of elastic collisions between trapped and free atoms on the quasi steady-state population of the trap, as well as the energy distribution and the coherence of the outcoupled atoms.Comment: 25 pages, 11 figures, to appear in J. Phys.

Resonance fluorescence in a band gap material: Direct numerical simulation of non-Markovian evolution

A numerical method of calculating the non-Markovian evolution of a driven atom radiating into a structured continuum is developed. The formal solution for the atomic reduced density matrix is written as a Markovian algorithm by introducing a set of additional, virtual density matrices which follow, to the level of approximation of the algorithm, all the possible trajectories of the photons in the electromagnetic field. The technique is perturbative in the sense that more virtual density matrices are required as the product of the effective memory time and the effective coupling strength become larger. The number of density matrices required is given by $3^{M}$ where $M$ is the number of timesteps per memory time. The technique is applied to the problem of a driven two-level atom radiating close to a photonic band gap and the steady-state correlation function of the atom is calculated.Comment: 14 pages, 9 figure

Nocturia as an Unrecognized Symptom of Uncontrolled Hypertension in Black Men Aged 35 to 49 Years.

Background Hypertension is assumed to be asymptomatic. Yet, clinically significant nocturia (≥2 nightly voids) constitutes a putative symptom of uncontrolled hypertension. Black men with hypertension may be prone to nocturia because of blunted nocturnal blood pressure ( BP ) dipping, diuretic drug use for hypertension, and comorbidity that predisposes to nocturia. Here, we test the hypothesis that nocturia is a common and potentially reversible symptom of uncontrolled hypertension in black men. Methods and Results We determined the strength of association between nocturia (≥2 nightly voids) and high BP (≥135/85 mm Hg) by conducting in-person health interviews and measuring BP with an automated monitor in a large community-based sample of black men in their barbershops. Because nocturia is prevalent and steeply age-dependent after age 50 years, we studied men aged 35 to 49 years. Among 1673 black men (mean age, 43±4 years [ SD ]), those with hypertension were 56% more likely than men with normotension to have nocturia after adjustment for diabetes mellitus and sleep apnea (adjusted odds ratio, 1.56; 95% CI , 1.25-1.94 [ P<0.0001]). Nocturia prevalence varied by hypertension status, ranging from 24% in men with normotension to 49% in men whose hypertension was medically treated but uncontrolled. Men with untreated hypertension were 39% more likely than men with normotension to report nocturia ( P=0.02), whereas men whose hypertension was treated and controlled were no more likely than men with normotension to report nocturia ( P=0.69). Conclusions Uncontrolled hypertension was an independent determinant of clinically important nocturia in a large cross-sectional community-based study of non-Hispanic black men aged 35 to 49 years. Clinical Trial Registration URL : http://www.clinicaltrials.gov . Unqiue identifier: NCT 02321618

Quantum dynamical theory for squeezing the output of a Bose-Einstein condensate

A linear quantum dynamical theory for squeezing the output of the trapped Bose-Einstein condensate is presented with the Bogoliubov approximation. We observe that the non-classical properties, such as sub-Poisson distribution and quadrature squeezing effect, mutually oscillate between the quantum states of the applied optical field and the resulting atom laser beam with time. In particular, it is shown that an initially squeezed optical field will lead to squeezing in the outcoupled atomic beam at later times.Comment: 6 pages, Latex file, Phys.Rev.A 63(2001)1560

Escape from a metastable well under a time-ramped force

Thermally activated escape of an over-damped particle from a metastable well under the action of a time-ramped force is studied. We express the mean first passage time (MFPT) as the solution to a partial differential equation, which we solve numerically for a model case. We discuss two approximations of the MFPT, one of which works remarkably well over a wide range of loading rates, while the second is easy to calculate and can provide a valuable first estimate.Comment: 9 pages, including 2 figure