In the ICEBERG project at UC Berkeley, we are developing an Internet-based integration of telephony and data services spanning diverse access networks. Our primary goals extensibility, scalability, robustness, personalized communication. We leverage Internet's low cost entry for service creation, provision, deployment, integration. present our solutions to signaling, easy resource reservation, admission control, billing, security in network architecture.

Results from condensed phase ab initio molecular dynamics (AIMD) simulations suggest a proton transfer reaction is facilitated by "presolvation" in which the hydronium transiently solvated four water molecules, similar to typical solvation structure of water, accepting weak hydrogen bond fourth molecule. A new version 3.2 multistate empirical valence (MS-EVB 3.2) model for hydrated excess incorporating this presolvation behavior therefore developed. The classical MS-EVB show structural...

Water's ability to donate and accept hydrogen bonds leads unique complex collective dynamical phenomena associated with its hydrogen-bond network. It is appreciated that the vibrations governing liquid water's molecular dynamics are delocalized, nuclear motion evolving coherently over span of several molecules. Using two-dimensional infrared spectroscopy, we have found motions heavy water, D2O, qualitatively different than those H2O. The nonlinear spectrum D2O reveals distinct O–D stretching...

The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it powerful tool for investigating the and dynamics excess protons in water. Although significant interest, line broadening that results from ultrafast evolution different solvated proton-water structures assignment liquid-phase IR spectra challenging task. In this work, we apply normal mode analysis using density functional theory thousands clusters taken reactive molecular trajectories...

Liquid water’s rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies OH stretching excitations H2O indicate that they are delocalized over several molecules, raising questions about whether bending vibrations similarly delocalized. In this paper, we take advantage an improved 50 fs time-resolution broadband infrared (IR) spectroscopy to interrogate 2D IR lineshape...

Several recent mass spectrometry experiments reveal a marked enhancement of the reaction rate organic reactions in microdroplets. This has been tentatively attributed to accumulation excess charge on surface, which turn can give rise lowering activation energy reaction. Here we model droplets as three-step process: (i) diffusion reactant from core droplet (ii) search by surface find reactive partner, and finally (iii) intrinsic leading bond breaking product formation. We obtain analytic...

The catalytic conversion of adenosine triphosphate (ATP) and monophosphate (AMP) to diphosphate (ADP) by adenylate kinase (ADK) involves large amplitude, ligand induced domain motions, involving the opening closing ATP binding (LID) AMP (NMP) domains, during repeated cycle. We discover analyze an interesting dynamical coupling between motion two domains opening, using scale atomistic molecular dynamics trajectory analysis, covariance multidimensional free energy calculations with explicit...

Rugged energy landscapes find wide applications in diverse fields ranging from astrophysics to protein folding. We study the dependence of diffusion coefficient (D) a Brownian particle on distribution width (ɛ) randomness Gaussian random landscape by simulations and theoretical analysis. first show that elegant expression Zwanzig [Proc. Natl. Acad. Sci. U.S.A. 85, 2029 (1988)] for D(ɛ) can be reproduced exactly using Rosenfeld diffusion-entropy scaling relation. Our Zwanzig's overestimates D...

Layer-wise, distance-dependent orientational relaxation of water confined in reverse micelles (RM) is studied using theoretical and computational tools. We use both a newly constructed “spins on ring” (SOR) Ising-type model (with Shore-Zwanzig rotational dynamics) atomistic simulations with explicit water. Our study explores the effect micelle size role intermolecular correlations, compromised by presence highly polar surface, distance (from interface) dependence relaxation. The can capture...

In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small a macroscopic scale. Examples include lipid bilayers and reverse micelles as well biomolecules like proteins, DNA zeolites, to name few. While presence interfaces interrupts continuous hydrogen bond network liquid water, confinement mesoscopic introduces new features. Even when molecular scale, natural biological have features (like charge, hydrophobicity) vary diameter water....

Infrared (IR) spectroscopy of the water O-H stretch has been widely used to probe both local hydrogen-bonding structure and dynamics aqueous systems. Although significant interest, IR excess protons in remains difficult assign as a result extensive strong intermolecular interactions hydrated proton complexes. As an alternate approach, we develop mixed quantum-classical model for vibrational isotopically dilute that draws on frozen proton-water clusters taken from reactive molecular...

We present computer simulation study of two-dimensional infrared spectroscopy (2D-IR) water confined in reverse micelles (RMs) various sizes. The is motivated by the need to understand altered dynamics performing layerwise decomposition water, with an aim quantify relative contributions different layers molecules calculated 2D-IR spectrum. 0-1 transition spectra clearly show substantial elongation, due inhomogeneous broadening and incomplete spectral diffusion, along diagonal surface layer...

We study melting of a face-centered crystalline solid consisting polydisperse Lennard-Jones spheres with Gaussian polydispersity in size. The phase diagram reproduces the existence nearly temperature invariant terminal (δ(t) =/~ 0.11), no signature reentrant melting. absence can be attributed to influence attractive part potential upon find that at fractional density change approaches zero, which seems arise from vanishingly small compressibility disordered phase. At constant and volume...

We examine the separation distance dependence of hydrophobic force by systematically varying (d) between two walls. The exhibits a mediated crossover from liquid-like to gas-like behavior at around d ∼ 12 Å for 1 atm pressure. can be fitted bi-exponential form, with longer part displaying correlation length 20 Å. In addition, is found accompanied divergent-like growth local relative number fluctuation water molecules confined surfaces. Furthermore, fixed (d = Å), we observe pressure induced...

The molecular-level understanding of the hydration structure external solutes is extremely challenging. In context molecular simulation, particularly sampling proper solvation by classical force fields remains always a matter concern. present work, we use theoretical vibrational spectroscopy to understand microscopic TMAO in water cases five different TMAO. We find that Netz (J. Phys. Chem. B 2013, 117, 8310–8321) field agrees better with experimental results. also observe O–H stretching...

Metalloproteins make up a class of proteins that incorporate metal ions into their structures, enabling them to perform essential functions in biological systems, such as catalysis and electron transport. Azurin is one metalloprotein with copper cofactor, having β-barrel structure exceptional thermal stability. The ion coordinated at end the structure, there disulfide bond opposite end. In this study, we explore effect high stability azurin by analyzing both native S–S bonded nonbonded (S–S...

We utilized linear and 2D infrared spectroscopy to analyze the carbonyl stretching modes of small esters in different solvents. Particularly noteworthy were distinct spectral line shapes aqueous solutions, prompting our investigation underlying factors responsible for these differences. Through experimental theoretical calculations, we identified presence hydrogen-bond-induced Fermi resonance as primary contributor varied solutions. Furthermore, findings revealed that skeletal deformation...

Experiments and computer simulation studies have revealed existence of rich dynamics in the orientational relaxation molecules confined systems such as water reverse micelles, cyclodextrin cavities, nanotubes. Here we introduce a novel finite length one dimensional Ising model to investigate propagation annihilation dynamical correlations understand intriguing shortening time that has been reported for small sized micelles. In our model, two spins at end cells are oriented opposite...

Metal cofactors are critical centers for different biochemical processes of metalloproteins, and often, this metal coordination renders additional structural stability. In study, we explore the stability conferred by copper ion on azurin analyzing both apo holo forms using temperature replica exchange molecular dynamics (REMD) data. We find a 14 K decrease in denaturation (406 K) relative to that (420 K), indicating ion-induced thermal azurin. The unfolding begins with melting α-helix...

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but also intrinsic to the thermodynamic nature of solution itself (like binary mixtures or at gas-liquid interface). The altered dynamics water presence such diverse surfaces has attracted considerable attention recent years. As these interfaces are quite narrow, only a few molecular layers...

Hydrophobic solutes significantly alter the water hydrogen bond network. The local alteration of solvation structures gets reflected in vibrational spectroscopic signal. Although it is possible to detect this microscopic feature by modern infrared spectroscopy, bulk phase spectra often come with a formidable challenge establishing connection experimental molecular structures. Theoretical spectroscopy can serve as more powerful tool where data cannot provide picture. In present work, we build...