arXiv subjects

Sahand Jamal Rahi

Publications and source records attributed to Sahand Jamal Rahi.

14 recordsLinked to original sources

arXiv2024

The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging.

eess.IV↗

arXiv2011

Electromagnetic Casimir Forces of Parabolic Cylinder and Knife-Edge Geometries

An exact calculation of electromagnetic scattering from a perfectly conducting parabolic cylinder is employed to compute Casimir forces in several configurations. These include interactions between a parabolic cylinder and a plane, two parabolic cylinders, and a parabolic cylinder and an ordinary cylinder. To elucidate the effect of boundaries, special attention is focused on the "knife-edge" limit in which the parabolic cylinder becomes a half-plane. Geometrical effects are illustrated by considering arbitrary rotations of a parabolic cylinder around its focal axis, and arbitrary translations perpendicular to this axis. A quite different geometrical arrangement is explored for the case of an ordinary cylinder placed in the interior of a parabolic cylinder. All of these results extend simply to nonzero temperatures.

quant-ph↗

arXiv2010

Casimir potential of a compact object enclosed by a spherical cavity

We study the electromagnetic Casimir interaction of a compact object contained inside a closed cavity of another compact object. We express the interaction energy in terms of the objects' scattering matrices and translation matrices that relate the coordinate systems appropriate to each object. When the enclosing object is an otherwise empty metallic spherical shell, much larger than the internal object, and the two are sufficiently separated, the Casimir force can be expressed in terms of the static electric and magnetic multipole polarizabilities of the internal object, which is analogous to the Casimir-Polder result. Although it is not a simple power law, the dependence of the force on the separation of the object from the containing sphere is a universal function of its displacement from the center of the sphere, independent of other details of the object's electromagnetic response. Furthermore, we compute the exact Casimir force between two metallic spheres contained one inside the other at arbitrary separations. Finally, we combine our results with earlier work on the Casimir force between two spheres to obtain data on the leading order correction to the Proximity Force Approximation for two metallic spheres both outside and within one another.

quant-ph↗

arXiv2010

Casimir force between sharp-shaped conductors

Casimir forces between conductors at the sub-micron scale cannot be ignored in the design and operation of micro-electromechanical (MEM) devices. However, these forces depend non-trivially on geometry, and existing formulae and approximations cannot deal with realistic micro-machinery components with sharp edges and tips. Here, we employ a novel approach to electromagnetic scattering, appropriate to perfect conductors with sharp edges and tips, specifically to wedges and cones. The interaction of these objects with a metal plate (and among themselves) is then computed systematically by a multiple-scattering series. For the wedge, we obtain analytical expressions for the interaction with a plate, as functions of opening angle and tilt, which should provide a particularly useful tool for the design of MEMs. Our result for the Casimir interactions between conducting cones and plates applies directly to the force on the tip of a scanning tunneling probe; the unexpectedly large temperature dependence of the force in these configurations should attract immediate experimental interest.

quant-ph↗

arXiv2010

Geometry and material effects in Casimir physics - Scattering theory

We give a comprehensive presentation of methods for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, to nonzero temperatures, and to spatial arrangements in which one object is enclosed in another. Our method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects. This approach, which combines methods of statistical physics and scattering theory, is well suited to analyze many diverse phenomena. We illustrate its power and versatility by a number of examples, which show how the interplay of geometry and material properties helps to understand and control Casimir forces. We also examine whether electrodynamic Casimir forces can lead to stable levitation. Neglecting permeabilities, we prove that any equilibrium position of objects subject to such forces is unstable if the permittivities of all objects are higher or lower than that of the enveloping medium; the former being the generic case for ordinary materials in vacuum.

quant-ph↗

arXiv2010

Casimir Force at a Knife's Edge

The Casimir force has been computed exactly for only a few simple geometries, such as infinite plates, cylinders, and spheres. We show that a parabolic cylinder, for which analytic solutions to the Helmholtz equation are available, is another case where such a calculation is possible. We compute the interaction energy of a parabolic cylinder and an infinite plate (both perfect mirrors), as a function of their separation and inclination, $H$ and $θ$, and the cylinder's parabolic radius $R$. As $H/R\to 0$, the proximity force approximation becomes exact. The opposite limit of $R/H\to 0$ corresponds to a semi-infinite plate, where the effects of edge and inclination can be probed.

quant-ph↗

arXiv2009

Constraints on stable equilibria with fluctuation-induced forces

We examine whether fluctuation-induced forces can lead to stable levitation. First, we analyze a collection of classical objects at finite temperature that contain fixed and mobile charges, and show that any arrangement in space is unstable to small perturbations in position. This extends Earnshaw's theorem for electrostatics by including thermal fluctuations of internal charges. Quantum fluctuations of the electromagnetic field are responsible for Casimir/van der Waals interactions. Neglecting permeabilities, we find that any equilibrium position of items subject to such forces is also unstable if the permittivities of all objects are higher or lower than that of the enveloping medium; the former being the generic case for ordinary materials in vacuum.

quant-ph↗

arXiv2009

Casimir interactions of an object inside a spherical metal shell

We investigate the electromagnetic Casimir interactions of an object contained within an otherwise empty, perfectly conducting spherical shell. For a small object we present analytical calculations of the force, which is directed away from the center of the cavity, and the torque, which tends to align the object opposite to the preferred alignment outside the cavity. For a perfectly conducting sphere as the interior object, we compute the corrections to the proximity force approximation (PFA) numerically. In both cases the results for the interior configuration match smoothly onto those for the corresponding exterior configuration.

quant-ph↗

arXiv2009

Casimir spring and compass: Stable levitation and alignment of compact objects

We investigate a stable Casimir force configuration consisting of an object contained inside a spherical or spheroidal cavity filled with a dielectric medium. The spring constant for displacements from the center of the cavity and the dependence of the energy on the relative orientations of the inner object and the cavity walls are computed. We find that the stability of the force equilibrium can be predicted based on the sign of the force, but the torque cannot be.

cond-mat.stat-mech↗

arXiv2009

Scattering Theory Approach to Electrodynamic Casimir Forces

We give a comprehensive presentation of methods for calculating the Casimir force to arbitrary accuracy, for any number of objects, arbitrary shapes, susceptibility functions, and separations. The technique is applicable to objects immersed in media other than vacuum, nonzero temperatures, and spatial arrangements in which one object is enclosed in another. Our method combines each object's classical electromagnetic scattering amplitude with universal translation matrices, which convert between the bases used to calculate scattering for each object, but are otherwise independent of the details of the individual objects. The method is illustrated by re-deriving the Lifshitz formula for infinite half spaces, by demonstrating the Casimir-Polder to van der Waals cross-over, and by computing the Casimir interaction energy of two infinite, parallel, perfect metal cylinders either inside or outside one another. Furthermore, it is used to obtain new results, namely the Casimir energies of a sphere or a cylinder opposite a plate, all with finite permittivity and permeability, to leading order at large separation.

quant-ph↗

arXiv2008

Predicting Transcription Factor Specificity with All-Atom Models

The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites, rather than an ab initio approach. Here, we examine the possibility of using structure-based energy calculations that require no knowledge of bound sites but rather start with the structure of a protein-DNA complex. We study the PurR E. coli TF, and explore to which extent atomistic models of protein-DNA complexes can be used to distinguish between cognate and non-cognate DNA sites. Particular emphasis is placed on systematic evaluation of this approach by comparing its performance with bioinformatic methods, by testing it against random decoys and sites of homologous TFs. We also examine a set of experimental mutations in both DNA and the protein. Using our explicit estimates of energy, we show that the specificity for PurR is dominated by direct protein-DNA interactions, and weakly influenced by bending of DNA.

q-bio.BM↗

arXiv2008

Melting of persistent double-stranded polymers

Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a bubble. There is also bending stiffness at the branch points between the two segment types. The transfer matrix technique for single persistent chains is generalized to describe the branching bubbles. Properties of spherical harmonics are then exploited in truncating and numerically solving the resulting transfer matrix. This allows efficient computation of phase diagrams and force-extension curves (isotherms). While the main focus is on exposition of the transfer matrix technique, we provide general arguments for a reentrant melting transition in stiff double strands. Our theoretical approach can also be extended to study polymers with bubbles of any number of strands, with potential applications to molecules such as collagen.

cond-mat.soft↗

arXiv2008

Casimir forces between cylinders and plates

We study collective interaction effects that result from the change of free quantum electrodynamic field fluctuations by one- and two-dimensional perfect metal structures. The Casimir interactions in geometries containing plates and cylinders is explicitly computed using partial wave expansions of constrained path integrals. We generalize previously obtained results and provide a more detailed description of the technical aspects of the approach \cite{Emig06}. We find that the interactions involving cylinders have a weak logarithmic dependence on the cylinder radius, reflecting that one-dimensional perturbations are marginally relevant in 4D space-time. For geometries containing two cylinders and one or two plates, we confirm a previously found non-monotonic dependence of the interaction on the object's separations which does not follow from pair-wise summation of two-body forces. Qualitatively, this effect is explained in terms of fluctuating charges and currents and their mirror images.

cond-mat.stat-mech↗

arXiv2007

Nonmonotonic effects of parallel sidewalls on Casimir forces between cylinders

We analyze the Casimir force between two parallel infinite metal cylinders, with nearby metal plates (sidewalls), using complementary methods for mutual confirmation. The attractive force between cylinders is shown to have a nonmonotonic dependence on the separation to the plates. This intrinsically multi-body phenomenon, which occurs with either one or two sidewalls (generalizing an earlier result for squares between two sidewalls), does not follow from any simple two-body force description. We can, however, explain the nonmonotonicity by considering the screening (enhancement) of the interactions by the fluctuating charges (currents) on the two cylinders, and their images on the nearby plate(s). Furthermore, we show that this effect also implies a nonmonotonic dependence of the cylinder-plate force on the cylinder-cylinder separation.

cond-mat.stat-mech↗