Publications

2019
Ori Geuli, Qingli Hao, and Daniel Mandler. 2019. “One-step fabrication of NiOx-decorated carbon nanotubes-NiCo2O4 as an advanced electroactive composite for supercapacitors.” ELECTROCHIMICA ACTA, 318, Pp. 51-60.
Shahaf Zamir and Gideon Rahat. 2019. Online Political Personalization: A Comparative Study of Parties and Politicians in Israel. Jerusalem: Israel Democracy Institute. Publisher's Version
Ignacio Fdez. Galván, Morgane Vacher, Ali Alavi, Celestino Angeli, Francesco Aquilante, Jochen Autschbach, Jie J. Bao, Sergey I. Bokarev, Nikolay A. Bogdanov, Rebecca K. Carlson, Liviu F. Chibotaru, Joel Creutzberg, Nike Dattani, Mickaël G. Delcey, Sijia S. Dong, Andreas Dreuw, Leon Freitag, Luis Manuel Frutos, Laura Gagliardi, Frédéric Gendron, Angelo Giussani, Leticia González, Gilbert Grell, Meiyuan Guo, Chad E. Hoyer, Marcus Johansson, Sebastian Keller, Stefan Knecht, Goran Kovačević, Erik Källman, Giovanni Li Manni, Marcus Lundberg, Yingjin Ma, Sebastian Mai, João Pedro Malhado, Per Åke Malmqvist, Philipp Marquetand, Stefanie A. Mewes, Jesper Norell, Massimo Olivucci, Markus Oppel, Quan Manh Phung, Kristine Pierloot, Felix Plasser, Markus Reiher, Andrew M. Sand, Igor Schapiro, Prachi Sharma, Christopher J. Stein, Lasse Kragh Sørensen, Donald G. Truhlar, Mihkel Ugandi, Liviu Ungur, Alessio Valentini, Steven Vancoillie, Valera Veryazov, Oskar Weser, Tomasz A. Wesołowski, Per-Olof Widmark, Sebastian Wouters, Alexander Zech, J. Patrick Zobel, and Roland Lindh. 2019. “OpenMolcas: From Source Code to Insight.” Journal of Chemical Theory and ComputationJournal of Chemical Theory and Computation, 15, 11, Pp. 5925 - 5964. Publisher's Version Abstract

In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.

Overlapped embedded fragment stochastic density functional theory for covalently-bonded materials
Ming Chen, Roi Baer, Daniel Neuhauser, and Eran Rabani. 2019. “Overlapped embedded fragment stochastic density functional theory for covalently-bonded materials.” J. Chem. Phys., 150, 3, Pp. 034106. Publisher's Version Abstract

The stochastic density functional theory (DFT) [R. Baer et al., Phys. Rev. Lett. 111, 106402 (2013)] is a valuable linear-scaling approach to Kohn-Sham DFT that does not rely on the sparsity of the density matrix. Linear (and often sub-linear) scaling is achieved by introducing a controlled statistical error in the density, energy, and forces. The statistical error (noise) is proportional to the inverse square root of the number of stochastic orbitals and thus decreases slowly; however, by dividing the system into fragments that are embedded stochastically, the statistical error can be reduced significantly. This has been shown to provide remarkable results for non-covalently-bonded systems; however, the application to covalently bonded systems had limited success, particularly for delocalized electrons. Here, we show that the statistical error in the density correlates with both the density and the density matrix of the system and propose a new fragmentation scheme that elegantly interpolates between overlapped fragments. We assess the performance of the approach for bulk silicon of varying supercell sizes (up to Ne = 16 384 electrons) and show that overlapped fragments reduce significantly the statistical noise even for systems with a delocalized density matrix.

chen2018overlapped.pdf
The Dead Sea sedimentary fill is the basis for interpreting limnological conditions and regional paleo- hydrology. Such interpretations require an understanding of present-day hydroclimatology to reveal the relative impact of different atmospheric circulation patterns on water and sediment delivery to the Dead Sea. Here we address the most important meteorological conditions governing regional and local rain- storm occurrences, with different discharge characteristics. These meteorological controls over the Dead Sea watershed offer insights into past hydrometeorological processes that could have governed the Dead Sea water budget, seasonal and annual flows, floods, and the resultant sedimentology. Rainfall is typically associated with synoptic-scale circulation patterns forced by an upper-level trough that include Medi- terranean cyclones (MCs), active Red Sea troughs (ARSTs), and active subtropical jets (STJs), although other rainstorms and sub-synoptic processes also affect the region. We point to their relative importance in inflow volume, peak discharges, and delivery of sediments from the various environments of the basin. MCs control the annual water amount discharging into the Dead Sea. A change in their frequency, in- tensity, or latitude can substantially alter the lake water balance. A change in frequency or intensity of ARSTs and STJs affects extreme flood and sediment discharge. Floods reach the lake through (a) the Mediterranean-climate-controlled Lower Jordan River, (b) desert-climate-controlled Nahal HaArava, and (c) the arid wadies draining directly into the Dead Sea, some with wetter headwaters. Floods in the wetter parts of the watershed are mainly controlled by MCs, and characterized by larger frequency, volume, and duration, but lower peak discharges and possibly sediment delivery, than floods in the desert parts, which can be produced by the three synoptic types. ARSTs contribute to heavy rainfall, typically of a spotty nature, in the desert parts of the watershed. STJs are currently rare, but their rainfall accumulation may be greater than the annual mean over a broad area in the southern dry Dead Sea watershed. This article presents a review of recent studies, which is extended with new analyses of meteorological, rainfall and flood data, underlining the importance of the Lower Jordan River in sup- plying water volume to the Dead Sea, as compared to the high-discharge, low-volume floods of the arid part of the watershed. Our analyses will help interpret paleoenvironmental conditions in the Dead Sea sedimentary record, and cope with the region's changing climate.
Nicole Behar, Ron Shaar, Lisa Tauxe, Hanna Asefaw, Yael Ebert, Ariel Heimann, Anthony AP Koppers, and Hagai Ron. 2019. “Paleomagnetism and paleosecular variations from the Plio-Pleistocene Golan Heights volcanic plateau, Israel.” Geochemistry, Geophysics, Geosystems.
Eli Sobolev, Pavel Komm, Salman Noah, and Gilad Marcus. 2019. “Parametric amplification in large-aperture diffusion-bonded periodically poled crystals.” Opt. Lett., 44, 5, Pp. 1261–1264. Publisher's Version Abstract

With conventional poling techniques of pyroelectric crystals, the thickness of the periodically poled crystals is typically limited to 0.5&\#x2013;1&\#x00A0;mm. Such a small aperture of the crystal limits the amount of energy/power that this device may deliver. Here we discuss diffusion bonding as an alternative method to achieve a wider periodically poled crystal, with virtually unlimited width. It is shown that the amplified signal preserved a good beam profile despite a possible phase shift between the stitched crystals. This technique may be extended to larger aperture optical parametric amplifiers and allows for high energy output from periodically poled crystals.

Full_Text.pdf
2019. “Park, Gil-Sung and Otmazgin, Nissim. "Introduction: Fandom Formation and the Globalization of Hallyu".” In Transcultural Fandom and the Globalization of Hallyu. Korea University Press.
hallyi_book_cover.jpg
Jeremy Boger-Lombard and Ori Katz. 2019. “Passive optical time-of-flight for non line-of-sight localization.” Nature Communications, 10. Publisher's Version
Ruben Borg. 2019. “Past, Passivity, Passion: Deleuze's Allegorical Drama.” CounterText, 5, 1, Pp. 70-88. Publisher's Version Abstract
This article offers a rhetorical analysis of Deleuze’s concept of the past, understood not as a modification of the present but as a pre-predicative, non-subjective articulation of time. Focusing on the discussion of the three passive syntheses of time in Chapter 2 of Difference and Repetition, it traces the continuity between past, passivity and passion across Deleuze’s body of work in an effort not only to remark on the conceptual resonances between them, but, more importantly, to examine the figural and formal choices that codify those resonances, and to some extent over-determine them – in particular, Deleuze’s recourse to allegory and tragic form. Though the past is constituted as a primordial component of time, it already exceeds itself in the passivity of that constitutive moment, of that originary gesture by which it is first committed to historical experience. The process is rendered in dramatic terms: Habitus and Mnemosyne (Habit and Memory; Present and Past) are first pitted against each other – respectively, as the origin of time and its ground. They are then overthrown by an unnamed third element ‘which subordinates the other two to itself’ and opens the whole to infinity. The article thematises the significance of the past within this allegorical drama, develops the character, and draws out the temporal structures encoded in Deleuze’s figurations.
The peace dividend as an intangible benefit in mega-project justification: A comparative content analysis of the Dead Sea-Red Sea Canal

Large infrastructure schemes have become part of our landscape. Their controversial nature often requires elaborate justifications including the use of intangible benefits. One intangible benefit that has increasingly been raised in support of mega-projects is the peace dividend. Yet, to date, few studies have systematically addressed the following questions: to what extent, by whom, and in what ways is the peace dividend used as a strategic tool when it comes to justifying contested mega-projects? This article examines the use of different types of arguments in mega-project justification, with a focus on the peace dividend as a political intangible benefit. Through a comparative content analysis of coverage of the Dead Sea-Red Sea Canal project in Israeli and Jordanian news media, we illustrate how the peace dividend is employed as a framing device by both project supporters and opponents and how it is positioned in relation to other types of benefits and costs. We found that the marketing of contested mega-projects to public and political constituencies entails a variety of justifications, reflected in the various framing modes used to influence public opinion in both Israel and Jordan. The nature and intensity of these justifications are sensitive to the media environment and the degree of economic development. Our findings indicate that the peace dividend as a line of defense for the project is the most controversial of all other justification domains.

Is Planning Delay Really a Constraint in the Provision of Housing? Some Evidence from Israel
Ziv Rubin and Daniel Felsenstein. 2019. “Is Planning Delay Really a Constraint in the Provision of Housing? Some Evidence from Israel.” Papers in Regional Science, 98, 5, Pp. 2179-2200. Publisher's Version Abstract

This paper revisits the claim that a causal link exists between the inflexibility of land‐use planning and low elasticity of housing supply. A theoretical model of factors impacting district‐level planning is presented alongside a model of the impact of planning delay on housing supply. The models are estimated for the Tel Aviv district using detailed data covering a 12‐year period. Results show significant impacts on planning delay due to plan, municipality and district planning commission characteristics. House prices exert a positive effect on planning speed and municipal funding acts as a supply constraint. While planning delay does not impact housing supply, delay uncertainty has a negative impact and acts as a constraint.

Polyphenols Inhibit Candida albicans and Streptococcus mutans Biofilm Formation.
Yogi Farkash, Mark Feldman, Isaac Ginsburg, Doreen Steinberg, and Miriam Shalish. 2019. “Polyphenols Inhibit Candida albicans and Streptococcus mutans Biofilm Formation..” Dentistry Journal , 7, 2. Publisher's Version Abstract

Background:Streptococcus mutans (S. mutans) and Candida albicans (C. albicans) are two major contributors to dental caries. They have a symbiotic relationship, allowing them to create an enhanced biofilm. Our goal was to examine whether two natural polyphenols (Padma hepaten (PH) and a polyphenol extraction from green tea (PPFGT)) could inhibit the caries-inducing properties of S. mutans and C. albicans. Methods: Co-species biofilms of S. mutans and C. albicans were grown in the presence of PH and PPFGT. Biofilm formation was tested spectrophotometrically. Exopolysaccharides (EPS) secretion was quantified using confocal scanning laser microscopy. Biofilm development was also tested on orthodontic surfaces (Essix) to assess biofilm inhibition ability on such an orthodontic appliance. Results: PPFGT and PH dose-dependently inhibited biofilm formation without affecting the planktonic growth. We found a significant reduction in biofilm total biomass using 0.625 mg/mL PPFGT and 0.16 mg/mL PH. A concentration of 0.31 mg/mL PPFGT and 0.16 mg/mL PH inhibited the total cell growth by 54% and EPS secretion by 81%. A reduction in biofilm formation and EPS secretion was also observed on orthodontic PVC surfaces. Conclusions: The polyphenolic extractions PPFGT and PH have an inhibitory effect on S. mutans and C. albicans biofilm formation and EPS secretion.

dentistry-07-00042-v2.pdf
Daniel McGraw, Efthymios I. Nikolopoulos, Francesco Marra, and Emmanouil N. Anagnostou. 2019. “Precipitation frequency analyses based on radar estimates: An evaluation over the contiguous United States.” Journal of Hydrology. Publisher's Version Abstract
The lack of knowledge on precipitation frequency over ungauged areas introduces a significant source of uncertainty in relevant engineering designs and risk estimation procedures. Radar-based observations offer precipitation information over ungauged areas and thus have gained increasing attention as a potential solution to this problem. However, due to their relative short data records and inherent uncertainty sources, their ability to provide accurate estimates on the frequency of precipitation extremes requires evaluation. This study involves the evaluation of at-site precipitation frequency estimates from NEXRAD Stage IV radar precipitation dataset. We derive precipitation annual maxima series from the 16yrs record (2002-2017) of NEXRAD and we compare against 539 long-term (50yrs) hourly gauge records. In addition, Intensity-Duration-Frequency (IDF) curves are estimated from both radar and gauge dataset and compared. IDF estimation is based on fitting the Generalize Extreme Value distribution to annual precipitation maxima. Evaluation is carried out over the contiguous United States and results are grouped and presented for five dominant climate classes and for a range of return period and precipitation durations. NEXRAD was shown to overestimate intensities at shorter durations (1- and 3-hr) and low quantiles, while it tends to underestimate higher quantiles at longer durations (24hr). In addition, evaluation of the IDF curves estimated from NEXRAD revealed a distinct geographic dependence with certain regions exhibiting a tendency to overestimation (e.g. east of the Rocky Mountains) or underestimation (Midwest). Overall, this analysis suggests that, while significant discrepancies may exist, there are several cases where NEXRAD provide estimates within the uncertainty bounds of the reference rain gauge dataset. The climate/geographic region and the temporal duration are important aspects to consider. Findings provided in this work on these aspects will hopefully serve as a general guideline for those interested in using NEXRAD estimates for further research or applications on precipitation extremes.
Francesco Marra, Efthymios I. Nikolopoulos, Emmanouil N. Anagnostou, András Bárdossy, and Efrat Morin. 2019. “Precipitation frequency analysis from remotely sensed datasets: A focused review.” Journal of Hydrology, 574, October 2018, Pp. 699–705. Publisher's Version Abstract
Information on extreme precipitation is essential to managing weather-related risks and designing hydraulic structures. Research attention to frequency analyses based on remotely sensed precipitation datasets, such as those obtained from weather radars and satellites, has been rapidly increasing owing to their potential to provide information for ungauged regions worldwide. Together with the ability to measure the areal scale directly, these analyses promise to overcome the sampling limitations of traditional methods based on rain gauges. This focused review of the literature depicts the state of the art after a decade of efforts, and identifies the crucial gaps in knowledge and methodology that currently hinder the quantitative use of remotely sensed datasets in water resources system design and operation. It concludes by highlighting a set of research directions promising immediate impact with regard to the separation of the sources of uncertainty currently affecting applications based on remotely sensed datasets, the development of statistical methods that can cope with the peculiar characteristics of these datasets, and the improvement of validation methods. Important gains in knowledge are expected from the explicit inclusion of the areal dimension in the analyses and from the fine-scale investigation of extreme precipitation climatology.
Honglong Shen, Xifeng Xia, Yu Ouyang, Xinyan Jiao, Sadaf Mutahir, Daniel Mandler, and Qingli Hao. 2019. “Preparation of Biomass-Based Porous Carbons with High Specific Capacitance for Applications in Supercapacitors.” CHEMELECTROCHEM, 6, 14, Pp. 3599-3605.
Pro-inflammatory agents released by pathogens, dying host cells, and neutrophils act synergistically to destroy host tissues: a working hypothesis

Abstract: We postulate that the extensive cell and tissue damage inflicted by many infectious, inflammatory and post-inflammatory episodes is an enled result of a synergism among the invading microbial agents, host neutrophils and dead and dying cells in the nidus. Microbial toxins and other metabolites along with the plethora of pro-inflammatory agents released from activated neutrophils massively recruited to the infectious sites and high levels of cationic histones, other cationic peptides, proteinases and Th1 cytokines released from activated polymorphonuclear neutrophils (PMNs) and from necrotized tissues may act in concert (synergism) to bring about cell killing and tissue destruction. Multiple, diverse interactions among the many potential pro-inflammatory moieties have been described in these complex lesions. Such infections are often seen in the skin and aerodigestive tract where the tissue is exposed to the environment, but can occur in any tissue. Commonly, the tissue-destructive infections are caused by group A streptococci, pneumococci, Staphylococcus aureus, meningococci, Escherichia coli and Shigella, although many other microbial species are seen on occasion. All these microbial agents are characterized by their ability to recruit large numbers of PMNs. Given the complex nature of the disease process, it is proposed that, to treat these multifactorial disorders, a “cocktail” of anti-inflammatory agents combined with non-bacteriolytic antibiotics and measures to counteract the critical toxic role of cationic moieties might prove more effective than a strategy based on attacking the bacteria alone.

jir-190007-pro-inflammatory-agents-released-by-pathogens-by-dying-host-012219.pdf
2019. “publications”.
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Christian Wiebeler and Igor Schapiro. 2019. “QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra.” Molecules, 24, 9. Publisher's Version Abstract
Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes.

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