Alexander Tenenbaum

Bio: Alexander Tenenbaum is an academic researcher from Sapienza University of Rome. The author has contributed to research in topics: Coherence (statistics) & Molecular dynamics. The author has an hindex of 13, co-authored 36 publications receiving 618 citations. Previous affiliations of Alexander Tenenbaum include University of Paris & University of Padua.

Stationary nonequilibrium states by molecular dynamics. Fourier's law

Abstract: We have developed a technique to produce stationary nonequilibrium states in a molecular-dynamics system; this method is based on the introduction of stochastic boundary conditions to simulate the contact with a thermal wall. The relaxation times involved in such contact are short enough (\ensuremath{\sim}${10}^{\ensuremath{-}11}$ sec) to make the technique suitable for computer experiments. The method allows the simulation of bulk properties in a system coupled with a heat reservoir and the study of the local thermodynamical equilibrium. Furthermore, it gives a physical description of the heat transfer near a thermal wall. The method has been applied to simulate high thermal gradients in a region of dense fluids ranging from the gas-liquid coexistence line to the freezing line, to check the validity of the linear thermal response (Fourier's law). We have found that the linear region extends at least up to gradients of the order of 1.8\ifmmode\times\else\texttimes\fi{}${10}^{9}$ K/cm for argon. In the bulk region where boundary effects are negligible we have verified the validity of the local equilibrium hypothesis for all simulated gradients.

Canonical ensemble and nonequilibrium states by molecular dynamics

Abstract: We present a new technique to simulate the contact of a molecular dynamics system with a thermal wall. A canonical ensemble is obtained, and its statistical and thermodynamic fluctuations are studied. The values of the specific heat found by simulation agree with the experimental data. By means of thermal walls at different temperatures, thermal gradients are obtained. The values of the thermal conductivity are consistent with the experimental data.

The use of a pair potential for the study of defects and disorder in aluminium

Abstract: The authors have examined the usefulness of the Dagens, Rasolt and Taylor (DRT) interionic potential (1975) for calculating disorder and defect properties in Al from the point of view of a molecular dynamics (MD) computer simulation. The problem was complicated by the strong long-range oscillations present in the Al potential and careful attention was paid to this detail. The authors confirmed that the low-temperature phonons generated by the MD program agreed very well with the quasi-harmonic phonons of DRT and then proceeded to generate the high-temperature phonons. They also calculated the liquid structure factor obtaining satisfactory agreement with experiment. They found, not too surprisingly, that the calculated vacancy formation energy for Al was much smaller than experiment by about 0.5 eV. However they noted that if one allows for re-screening effects in the vicinity of the vacancy a subtle three-body force comes into play which, on a crude argument, accounts for this difference.

Stochastic transition in two-dimensional Lennard-Jones systems

Abstract: We study by computer simulation the behavior at low energy of two-dimensional Lennard-Jones systems, with square or triangular cells and a number of degrees of freedom $N$ up to 128. These systems exhibit a transition from ordered to stochastic motions, passing through a region of intermediate behavior. We thus find two stochasticity borders, which separate in the phase space the ordered, intermediate, and stochastic regions. The corresponding energy thresholds have been determined as functions of the frequency $\ensuremath{\omega}$ of the initially excited normal modes; they generally increase with $\ensuremath{\omega}$ and appear to be independent of $N$. Their values agree with those found by other authors for one-dimensional LJ systems. We computed also the maximal Lyapunov characteristic exponent ${\ensuremath{\chi}}^{*}$ of our systems, which is a typical measure of stochasticity; this analysis shows that even in the ordered region certain stochastic features may persist. At higher energies, ${\ensuremath{\chi}}^{*}$ increases linearly with the energy per degree of freedom $e$. The law ${\ensuremath{\chi}}^{*}(e)$ has been determined in the thermodynamic limit by extrapolation. The values found for the stochasticity thresholds fall in a physically significant energy range. The behavior of the thresholds as a function of $\ensuremath{\omega}$ and $N$ is compatible with the hypothesis on the existence of a classical zero-point energy, advanced by Cercignani, Galgani, and Scotti.

Continuous thermal collapse of the intrinsically disordered protein tau is driven by its entropic flexible domain.

Abstract: The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state lack a folded structure and fluctuate between many conformations. In its physiological state, tau helps nucleating and stabilizing the microtubules’ (MTs) surfaces in the axons of the neurons. Tau is mainly composed by two domains: (i) the binding domain that tightly bounds the MT surfaces and (ii) the projection domain that exerts a long-range entropic repulsive force and thus provides the proper spacing between adjacent MTs. Tau is also involved in the genesis and in the development of the Alzheimer disease when it detaches from MT surfaces and aggregates in paired helical filaments. Unfortunately, the molecular mechanisms behind these phenomena are still unclear. Temperature variation, rarely considered in biological studies, is here used to provide structural information on tau correlated to its role as an entropic spacer between adjacent MTs surfaces. In this paper, by means of small-angle ...

Molecular dynamics with coupling to an external bath.

Abstract: In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints The influence of coupling time constants on dynamical variables is evaluated A leap‐frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath

Intrinsically Disordered Proteins

Abstract: Nothing is solid about proteins. Governing rules and established laws are constantly broken. As an example, the last decade and a half have witnessed the fall of one of the major paradigms in structural biology. Contrarily to the more than a century-old belief that the unique function of a protein is determined by its unique structure, which, in its turn, is defined by the unique amino acid sequence, many biologically active proteins lack stable tertiary and/or secondary structure either entirely or at their significant parts. Such intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered domains and functional IDP regions (IDPRs) are highly abundant in nature, and many of them are associated with various human diseases. Such disordered proteins and regions are very different from ordered and well-structured proteins and domains at a variety of levels and possess well-recognizable biases in their amino acid compositions and amino acid sequences. A characteristic feature of these proteins is their exceptional structural heterogeneity, where different parts of a given polypeptide chain can be ordered (or disordered) to different degrees. As a result, a typical IDP/IDPR contains a multitude of potentially foldable, partially foldable, differently foldable or not foldable structural segments. This distribution of conformers is constantly changing in time, where a given segment of a protein molecule has different structures at different time points. The distribution is also constantly changing in response to changes in the environment. This mosaic structural organization is crucial for their functions and many IDPs are engaged in biological functions that rely on high conformational flexibility and that are not accessible to proteins with unique and fixed structures. As a result, the functional repertoire of IDPs complements that of ordered proteins, with IDPs/IDPRs being often involved in regulation, signaling and control. This Sprenger Briefs volume is dedicated to IDPs and IDPRs and an attempt is made to compress a massive amount of knowledge and into a digest that aims to be of use to those wishing a fast entry into this promising field of structural biology.