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Jef Wagner

Publications and source records attributed to Jef Wagner.

At least 19 recordsLinked to original sources
arXiv2017

Impact of a non-uniform charge distribution on virus assembly

Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive domains on the virus coat proteins and the negative genome. We model the effect of the icosahedral charge distribution from the protein shell instead of uniform using a mean-field theory. We find that the non-uniform charge distribution strongly affects the optimal genome length, and that it can explain the experimentally observed phenomenon of overcharging of virus and virus-like particles.

physics.bio-ph↗
arXiv2016

In vitro protease cleavage and computer simulations reveal the HIV-1 capsid maturation pathway

HIV-1 virions assemble as immature particles containing Gag polyproteins that are processed by the viral protease into individual components, resulting in the formation of mature infectious particles. There are two competing models for the process of forming the mature HIV-1 core: the disassembly and de novo reassembly model and the non-diffusional displacive model. To study the maturation pathway, we simulate HIV-1 maturation in vitro by digesting immature particles and assembled virus-like particles with recombinant HIV-1 protease and monitor the process with biochemical assays and cryoEM structural analysis in parallel. Processing of Gag in vitro is accurate and efficient and results in both soluble capsid protein and conical or tubular capsid assemblies, seemingly converted from immature Gag particles. Computer simulations further reveal probable assembly pathways of HIV-1 capsid formation. Combining the experimental data and computer simulations, our results suggest a sequential combination of both displacive and disassembly/reassembly processes for HIV-1 maturation.

physics.bio-ph↗
arXiv2016

Effects of RNA branching on the electrostatic stabilization of viruses

Many single-stranded (ss) RNA viruses self assemble from capsid protein subunits and the nucleic acid to form an infectious virion. It is believed that the electrostatic interactions between the negatively charged RNA and the positively charged viral capsid proteins drive the encapsidation, although there is growing evidence that the sequence of the viral RNA also plays a role in packaging. In particular the sequence will determine the possible secondary structures that the ssRNA will take in solution. In this work, we use a mean field theory to investigate how the secondary structure of the RNA combined with electrostatic interactions affects the efficiency of assembly and stability of the assembled virions. We show that the secondary structure of RNA may result in negative osmotic pressures while a linear polymer causes positive osmotic pressures for the same conditions. This may suggest that the branched structure makes the RNA more effectively packaged and the virion more stable.

physics.bio-ph↗
arXiv2016

Role of Genome in the Formation of Conical Retroviral Shells

Human immunodeficiency virus (HIV) capsid proteins spontaneously assemble around the genome into a protective protein shell called the capsid, which can take on a variety of shapes broadly classified as conical, cylindrical and irregular. The majority of capsids seen in in vivo studies are conical in shape, while in vitro experiments have shown a preference for cylindrical capsids. The factors involved in the selection of the unique shape of HIV capsids are not well understood, and in particular the impact of RNA on the formation of the capsid is not known. In this work, we study the role of the genome and its interaction with the capsid protein by modeling the genomic RNA through a mean-field theory. Our results show that the confinement free energy for a homopolymeric model genome confined in a conical capsid is lower than that in a cylindrical capsid, at least when the genome does not interact with the capsid, which seems to be the case in in vivo experiments. Conversely, the confinement free energy for the cylinder is lower than for a conical capsid if the genome is attracted to the capsid proteins as the in vitro experiments. Understanding the factors that contribute to the formation of conical capsids may shed light on the infectivity of HIV particles.

physics.bio-ph↗
arXiv2016

Vacuum energy density and pressure near a soft wall

Perfectly conducting boundaries, and their Dirichlet counterparts for quantum scalar fields, predict nonintegrable energy densities. A more realistic model with a finite ultraviolet cutoff yields two inconsistent values for the force on a curved or edged boundary (the "pressure anomaly"). A still more realistic, but still easily calculable, model replaces the hard wall by a power-law potential; because it involves no a posteriori modification of the formulas calculated from the theory, this model should be anomaly-free. Here we first set up the formalism and notation for the quantization of a scalar field in the background of a planar soft wall, and we approximate the reduced Green function in perturbative and WKB limits (the latter being appropriate when either the mode frequency or the depth into the wall is sufficiently large). Then we display numerical calculations of energy density and pressure for the region outside the wall, which show that the pressure anomaly does not occur there. Calculations inside the wall are postponed to later papers, which must tackle regularization and renormalization of divergences induced by the potential in the bulk region.

hep-th↗
arXiv2016

RNA topology remolds electrostatic stabilization of viruses

Simple RNA viruses efficiently encapsulate their genome into a nano-sized protein shell: the capsid. Spontaneous co-assembly of the genome and the capsid proteins is driven predominantly by electrostatic interactions between the negatively charged RNA and the positively charged inner capsid wall. Using field theoretic formulation we show that the inherently branched RNA secondary structure allows viruses to maximize the amount of encapsulated genome and make assembly more efficient, allowing viral RNAs to out-compete cellular RNAs during replication in infected host cells.

physics.bio-ph↗
arXiv2015

Adsorption of annealed branched polymers on curved surfaces

The behavior of annealed branched polymers near adsorbing surfaces plays a fundamental role in many biological and industrial processes. Most importantly single stranded RNA in solution tends to fold up and self-bind to form a highly branched structure. Using a mean field theory, we both perturbatively and numerically examine the adsorption of branched polymers on surfaces of several different geometries in a good solvent. Independent of the geometry of the wall, we observe that as branching density increases, surface tension decreases. However, we find a coupling between the branching density and curvature in that a further lowering of surface tension occurs when the wall curves towards the polymer, but the amount of lowering of surface tension decreases when the wall curves away from the polymer. We find that for branched polymers confined into spherical cavities, most of branch-points are located in the vicinity of the interior wall and the surface tension is minimized for a critical cavity radius. For branch polymers next to sinusoidal surfaces, we find that branch-points accumulate at the valleys while end-points on the peaks.

cond-mat.soft↗
arXiv2014

The robust assembly of small symmetric nano-shells

Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells. Several studies have shown that symmetric shells appear in nature as a result of the free energy minimization of a generic interaction between their constituent subunits. We examine the physical basis for the formation of symmetric shells, and using a minimal model we demonstrate that these structures can readily grow from identical subunits under non equilibrium conditions. Our model of nano-shell assembly shows that the spontaneous curvature regulates the size of the shell while the mechanical properties of the subunit determines the symmetry of the assembled structure. Understanding the minimum requirements for the formation of closed nano-shells is a necessary step towards engineering of nano-containers, which will have far reaching impact in both material science and medicine.

cond-mat.soft↗
arXiv2014

Calculating Casimir interactions for Periodic Surface Relief Gratings using the C-Method

We develop a formalism to calculate the fluctuation-induced interactions in periodic systems. The formalism, which combines the scattering theory with the C method borrowed from electromagnetic gratings studies, is suitable and efficient for the calculation of the Casimir forces involving surface relief gratings. We apply the developed technique to obtain the energy and lateral force for simple 1-D sinusoidal gratings. Using this formalism we derived known asymptotic expressions that were previously obtained through perturbative approximations. At close separation, our numerical results match those obtained by the proximity force approximation and its first correction using the derivative expansion.

quant-ph↗
arXiv2013

Scattering Approach for Fluctuation--Induced Interactions at Fluid Interfaces

We develop the scattering formalism to calculate the interaction between colloidal particles trapped at a fluid interface. Since, in addition to the interface, the colloids may also fluctuate in this system, we implement the fluctuation of the boundaries into the scattering formalism and investigate how the interaction between colloids is modified by their fluctuations. This general method can be applied to any number of colloids with various geometries at an interface. We apply the formalism derived in this work to a system of spherical colloids at the interface between two fluid phases. For two spherical colloids, this method very effectively reproduces the previous known results. For three particles we find analytical expressions for the large separation asymptotic energies and numerically calculate the Casimir interaction at all separations. Our results show an interesting three body effect for fixed and fluctuating colloids. While the three body effect strengthens the attractive interaction between fluctuating colloids, it diminishes the attractive force between colloids fixed at an interface.

cond-mat.soft↗
arXiv2010

Exact Casimir energies at nonzero temperature: Validity of proximity force approximation and interaction of semitransparent spheres

In this paper, dedicated to the career of Tom Erber, we consider the Casimir interaction between weakly coupled bodies at nonzero temperature. For the case of semitransparent bodies, that is, ones described by delta-function potentials, we first examine the interaction between an infinite plane and an arbitrary curved surface. In weak coupling, such an interaction energy coincides with the exact form of the proximity force approximation obtained by summing the interaction between opposite surface elements at arbitrary temperature. This result generalizes a theorem proved recently by Decca et al. We also obtain exact closed-form results for the Casimir energy at arbitrary temperature for weakly coupled semitransparent spheres.

hep-th↗
arXiv2010

Casimir energy, dispersion, and the Lifshitz formula

Despite suggestions to the contrary, we show in this paper that the usual dispersive form of the electromagnetic energy must be used to derive the Lifshitz force between parallel dielectric media. This conclusion follows from the general form of the quantum vacuum energy, which is the basis of the multiple-scattering formalism. As an illustration, we explicitly derive the Lifshitz formula for the interaction between parallel dielectric semispaces, including dispersion, starting from the expression for the total energy of the system. The issues of constancy of the energy between parallel plates and of the observability of electrostrictive forces are briefly addressed.

cond-mat.other↗
arXiv2009

Casimir Effect for a Semitransparent Wedge and an Annular Piston

We consider the Casimir energy due to a massless scalar field in a geometry of an infinite wedge closed by a Dirichlet circular cylinder, where the wedge is formed by $δ$-function potentials, so-called semitransparent boundaries. A finite expression for the Casimir energy corresponding to the arc and the presence of both semitransparent potentials is obtained, from which the torque on the sidewalls can be derived. The most interesting part of the calculation is the nontrivial nature of the angular mode functions. Numerical results are obtained which are closely analogous to those recently found for a magnetodielectric wedge, with the same speed of light on both sides of the wedge boundaries. Alternative methods are developed for annular regions with radial semitransparent potentials, based on reduced Green's functions for the angular dependence, which allows calculations using the multiple-scattering formalism. Numerical results corresponding to the torque on the radial plates are likewise computed, which generalize those for the wedge geometry. Generally useful formulas for calculating Casimir energies in separable geometries are derived.

hep-th↗
arXiv2008

From multiple scattering to van der Waals interactions: exact results for eccentric cylinders

In this paper, dedicated to the career of Iver Brevik, we review the derivation of the retarded van der Waals or Casimir-Polder interaction between polarizable molecules from the general multiple scattering formulation of Casimir interactions between bodies. We then apply this van der Waals potential to examine the interaction between tenuous cylindrical bodies, including eccentric cylinders, and revisit the vanishing self-energy of a tenuous dielectric cylinder. In each case, closed-form expressions are obtained.

math-ph↗
arXiv2008

Weak Coupling Casimir Energies for Finite Plate Configurations

We derive and use an extremely simplified formula for the interaction Casimir energy for two separate bodies in the weak coupling regime for massless scalar fields. We derive closed form solutions for a general arrangement of two $δ$-function plates finite in one direction and infinite in another. We examine the situation of two parallel plates finite in both transverse directions.

hep-th↗
arXiv2008

Exact results for Casimir interactions between dielectric bodies: The weak-coupling or van der Waals Limit

In earlier papers we have applied multiple scattering techniques to calculate Casimir forces due to scalar fields between different bodies described by delta function potentials. When the coupling to the potentials became weak, closed-form results were obtained. We simplify this weak-coupling technique and apply it to the case of tenuous dielectric bodies, in which case the method involves the summation of van der Waals (Casimir-Polder) interactions. Once again exact results for finite bodies can be obtained. We present closed formulas describing the interaction between spheres and between cylinders, and between an infinite plate and a retangular slab of finite size. For such a slab, we consider the torque acting on it, and find non-trivial equilibrium points can occur.

hep-th↗