New Journal of Physics

Despite the vast progress and achievements in systems biology and integrative physiology in the last decades, there is still a significant gap in understanding the mechanisms through which (i) genomic, proteomic and metabolic factors and signaling pathways impact vertical processes across cells, tissues and organs leading to the expression of different disease phenotypes and influence the functional and clinical associations between diseases, and (ii) how diverse physiological systems and organs coordinate their functions over a broad range of space and time scales and horizontally integrate to generate distinct physiologic states at the organism level...

We theoretically explore a Rashba spin-orbit coupling scheme which operates entirely in the absolute ground state manifold of an alkali atom, thereby minimizing all inelastic processes. An energy gap between ground eigenstates of the proposed coupling can be continuously opened or closed by modifying laser polarizations. Our technique uses far-detuned 'Raman' laser coupling to create the Rashba potential, which has the benefit of low spontaneous emission rates. At these detunings, the Raman matrix elements that link m F magnetic sublevel quantum numbers separated by two are also suppressed...

We develop a theoretical framework to characterize the decoherence dynamics due to multi-photon scattering in an all-optical switch based on Rydberg atom induced nonlinearities. By incorporating the knowledge of this decoherence process into optimal photon storage and retrieval strategies, we establish optimized switching protocols for experimentally relevant conditions, and evaluate the corresponding limits in the achievable fidelities. Based on these results we work out a simplified description that reproduces recent experiments ( Nat...

We directly measured the normalized s -wave scattering cross-section of ultracold40 K atoms across a magnetic-field Feshbach resonance by colliding pairs of degenerate Fermi gases (DFGs) and imaging the scattered atoms. We extracted the scattered fraction for a range of bias magnetic fields, and measured the resonance location to be B 0 = 20.206(15) mT with width Δ = 1.0(5) mT. To optimize the signal-to-noise ratio of atom number in scattering images, we developed techniques to interpret absorption images in a regime where recoil induced detuning corrections are significant...

The segmentation of the vertebrate body plan during embryonic development is a rhythmic and sequential process governed by genetic oscillations. These genetic oscillations give rise to traveling waves of gene expression in the segmenting tissue. Here we present a minimal continuum theory of vertebrate segmentation that captures the key principles governing the dynamic patterns of gene expression including the effects of shortening of the oscillating tissue. We show that our theory can quantitatively account for the key features of segmentation observed in zebrafish, in particular the shape of the wave patterns, the period of segmentation and the segment length as a function of time...

Sorting of distinctly different cell types into specific tissue compartments has long been thought to be a problem in minimization of total free energy in immiscible fluids, wherein cell-cell adhesion, cell stiffness, and cell contraction combine to define an effective macroscopic tissue surface tension. Pawlizak et al. [11] now show not only that adhesion forces at interfaces unexpectedly fail to correlate with the density of adhesion molecules, but also that certain cancer cell lines unexpectedly fail to behave as a fluid, with cells becoming kinetically trapped in what might be a jammed, solid-like non-equilibrium state...

A number of novel experimental and theoretical results have recently been obtained on active soft matter, demonstrating the various interesting universal and anomalous features of this kind of driven systems. Here we consider the adhesion difference-driven segregation of actively moving units, a fundamental but still poorly explored aspect of collective motility. In particular, we propose a model in which particles have a tendency to adhere through a mechanism which makes them both stay in touch and synchronize their direction of motion - but the interaction is limited to particles of the same kind...

Ptychography is a powerful computational imaging technique that transforms a collection of low-resolution images into a high-resolution sample reconstruction. Unfortunately, algorithms that currently solve this reconstruction problem lack stability, robustness, and theoretical guarantees. Recently, convex optimization algorithms have improved the accuracy and reliability of several related reconstruction efforts. This paper proposes a convex formulation of the ptychography problem. This formulation has no local minima, it can be solved using a wide range of algorithms, it can incorporate appropriate noise models, and it can include multiple a priori constraints...

Despite considerable advances in understanding the molecular nature of cancer, many biophysical aspects of malignant development are still unclear. Here we study physical alterations of the surface of human cervical epithelial cells during stepwise in vitro development of cancer (from normal to immortal (premalignant), to malignant). We use atomic force microscopy to demonstrate that development of cancer is associated with emergence of simple fractal geometry on the cell surface. Contrary to the previously expected correlation between cancer and fractals, we find that fractal geometry occurs only at a limited period of development when immortal cells become cancerous; further cancer progression demonstrates deviation from fractal...

The Locus Coeruleus (LC) modulates cortical, subcortical, cerebellar, brainstem and spinal cord circuits and it expresses receptors for neuromodulators that operate in a time scale of several seconds. Evidences from anatomical, electrophysiological and optogenetic experiments have shown that LC neurons receive input from a group of neurons called Hypocretins (HCRTs) that release a neuropeptide called hypocretin. It is less known how these two groups of neurons can be coregulated using GABAergic neurons. Since the time scales of GABA A inhibition is several orders of magnitude faster than the hypocretin neuropeptide effect, we investigate the limits of circuit activity regulation using a realistic model of neurons...

To elucidate the nature of load sharing in the growth of multiple biopolymers, we perform stochastic simulations of the growth of biopolymer bundles against obstacles under a broad range of conditions and varying assumptions. The obstacle motion due to thermal fluctuations is treated explicitly. We assume the "Perfect Brownian Ratchet" (PBR) model, in which the polymerization rate equals the free-filament rate as soon as the filament-obstacle distance exceeds the monomer size. Accurate closed-form formulas are obtained for the case of a rapidly moving obstacle...

Molecular oxygen is indispensable for cellular viability and function. Hypoxia is a stress condition in which oxygen demand exceeds supply. Low cellular oxygen content induces a number of molecular changes to activate regulatory pathways responsible for increasing the oxygen supply and optimizing cellular metabolism under limited oxygen conditions. Hypoxia plays critical roles in the pathobiology of many diseases, such as cancer, heart failure, myocardial ischemia, stroke, and chronic lung diseases. Although the complicated associations between hypoxia and cardiovascular (and cerebrovascular) diseases (CVD) have been recognized for some time, there are few studies that investigate their biological link from a systems biology perspective...

Many cell movements occur via polymerization of the actin cytoskeleton beneath the plasma membrane at the front of the cell, forming a protrusion called a lamellipodium, while myosin contraction squeezes forward the back of the cell. In what is known as the "molecular clutch" description of cell motility, forward movement results from the engagement of the acto-myosin motor with cell-matrix adhesions, thus transmitting force to the substrate and producing movement. However during cell translocation, clutch engagement is not perfect, and as a result, the cytoskeleton slips with respect to the substrate, undergoing backward (retrograde) flow in the direction of the cell body...

Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance (EPS). Biofilms are harmful in many industries, and thus it is of great interest to understand their mechanical properties and structure to determine ways to destabilize them. By performing single particle tracking with beads of varying surface functionalization it was found that charge interactions play a key role in mediating mobility within biofilms. With a combination of single particle tracking and microrheological concepts, it was found that Escherichia coli biofilms display height dependent charge density that evolves over time...

Many cell types, including neurons, astrocytes and other cells of the central nervous system respond to changes in extracellular matrix or substrate viscoelasticity, and increased tissue stiffness is a hallmark of several disease states including fibrosis and some types of cancers. Whether the malignant tissue in brain, an organ that lacks the protein-based filamentous extracellular matrix of other organs, exhibits the same macroscopic stiffening characteristic of breast, colon, pancreatic, and other tumors is not known...

Biofilms are surface-associated conglomerates of bacteria that are highly resistant to antibiotics. These bacterial communities can cause chronic infections in humans by colonizing, for example, medical implants, heart valves, or lungs. Staphylococcus aureus, a notorious human pathogen, causes some of the most common biofilm-related infections. Despite the clinical importance of S. aureus biofilms, it remains mostly unknown how physical effects, in particular flow, and surface structure influence biofilm dynamics...

During the progression of pulmonary fibrosis, initially isolated regions of high stiffness form and grow in the lung tissue due to collagen deposition by fibroblast cells. We have previously shown that ongoing collagen deposition may not lead to significant increases in the bulk modulus of the lung until these local remodeled regions have become sufficiently numerous and extensive to percolate in a continuous path across the entire tissue [Bates et al. 2007 Am. J. Respir. Crit. Care Med. 176 617]. This model, however, did not include the possibility of spatially correlated deposition of collagen...

In this letter, we demonstrate a facile far-field approach to quantify the near-field local density of optical states (LDOS) of a nanorod using CdTe quantum dots (QDs) emitters tethered to the surface of nanorods as beacons for optical read-outs. Radiative decay rate was extracted to quantify the LDOS; our analysis indicates that the LDOS of the nanorod enhance both the radiative and nonradiative decay of QD, particularly radiative decay of QDs at the end of nanorod is enhanced by 1.17 times greater than that at the waist, while the nonradiative decay was uniformly enhanced over the nanorod...

The morphogenetic process of germ band retraction in Drosophila embryos involves coordinated movements of two epithelial tissues - germ band and amnioserosa. The germ band shortens along its rostral-caudal or head-to-tail axis, widens along its perpendicular dorsal-ventral axis, and uncurls from an initial 'U' shape. The amnioserosa mechanically assists this process by pulling on the crook of the U-shaped germ band. The amnioserosa may also provide biochemical signals that drive germ band cells to change shape in a mechanically autonomous fashion...

Multidimensional optical signals are commonly recorded by varying the delays between time ordered pulses. These control the evolution of the density matrix and are described by ladder diagrams. We propose a new non-time-ordered protocol based on following the time evolution of the wavefunction and described by loop diagrams. The time variables in this protocol allow to observe different types of resonances and reveal information about intraband dephasing not readily available by time ordered techniques. The time variables involved in this protocol become coupled when using entangled light, which provides high selectivity and background free measurement of the various resonances...