Christopher David Daub- Ph.D.
- PostDoc Position at University of Helsinki
Christopher David Daub
- Ph.D.
- PostDoc Position at University of Helsinki
Working hard in the data mines.
About
54
Publications
5,751
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1,086
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Introduction
Molecular dynamics simulations of aqueous systems, gas-phase systems, and in between (clusters, interfaces). Rare-events methods, external fields, non-equilibrium systems.
Current institution
Additional affiliations
August 2017 - present
November 2013 - present
October 2009 - September 2013
Publications
Publications (54)
We study pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models. Different pressures, electrolyte concentrations and pore sizes are examined. Our results indicate flow that deviates considerably from the predictions of Poi...
In this paper we study collisions between polyatomic radicals – an important process in fields ranging from biology to combustion. Energy transfer, formation of intermediate complexes and recombination reactions are treated, with applications to peroxy radicals in atmospheric chemistry. Multi-reference perturbation theory, supplemented by coupled-c...
Dimeric accretion products have been observed both in atmospheric aerosol particles and in the gas phase. With their low volatilities, they are key contributors to the formation of new aerosol particles, acting as seeds for more volatile organic vapors to partition onto. Many particle-phase accretion products have been identified as esters. Various...
We study the influence of an applied electric field on the structure and stability of some common bimolecular clusters that are found in the atmosphere. These clusters play an important role in new particle formation (NPF). For low values of the electric field (i.e., |E| ≤ 0.01 V Å–1), we demonstrate that the field response of the clusters can be p...
In recent work [Daub et al., ACS Earth Space Chem., 2022, 6, 2446] we have developed a simple model for describing the lifetime of pre-reactive complexes, and demonstrated its use for predicting the reactivity of barrierless reactions between peroxy radicals. Here, we modify and extend the method in three important ways. First, we compare the use o...
Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its...
Peroxy radicals are key intermediates in many atmospheric processes. Reactions between such radicals are of particular interest as they can lead to accretion products capable of participating in new particle formation (NPF). These reactions proceed through a tetroxide intermediate, which then decomposes to a complex of two alkoxy radicals and O2, w...
The oxidation of aromatics contributes significantly to the formation of atmospheric aerosol. Using toluene as an example, we demonstrate the existence of a molecular rearrangement channel in the oxidation mechanism. Based on both flow reactor experiments and quantum chemical calculations, we show that the bicyclic peroxy radicals (BPRs) formed in...
The oxidation of aromatics contributes significantly to the formation of atmospheric aerosol. Using toluene as an example, we demonstrate the existence of a novel molecular rearrangement channel in the oxidation mechanism. Based on both flow reactor experiments and quantum chemical calculations, we show that the bicyclic peroxy radicals (BPRs) form...
Proton transfer reaction (PTR) is a commonly applied ionization technique for mass spectrometers, in which hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later-generation PTR instruments have been designed for b...
Proton-transfer-reaction (PTR) is a commonly applied ionization technique for mass spectrometers, where hydronium ions (H3O+) transfer a proton to analytes with higher proton affinities than the water molecule. This method has most commonly been used to quantify volatile hydrocarbons, but later generation PTR-instruments have been designed for bett...
We propose to analyze molecular dynamics (MD) output via a supervised machine learning (ML) algorithm, the decision tree. The approach aims to identify the predominant geometric features which correlate with trajectories that transition between two arbitrarily defined states. The data-driven algorithm aims to identify these features without the bia...
We propose a supervised machine learning algorithm, decision trees, to analyze molecular dynamics output. The approach aims to identify the predominant geometric features which correlate with trajectories that transition between two arbitrarily defined states. The data-based algorithm aims to identify such features in an approach which is unbiased...
Atmospheric reactions, hitherto studied computationally mainly with static computations in conjunction with transition state theories, can be further described via path sampling calculations. Here we report on an exploratory study of the formic acid catalysed hydrolysis of SO 3 to produce H 2 SO 4 . We demonstrate that precise measurements of rate...
The deprotonation of formic acid is investigated using metadynamics in tandem with Born-Oppenheimer molecular dynamics (BOMD) simulations. We compare our findings for formic acid in pure water with previous studies before examining formic acid in aqueous solutions of lithium bromide. We carefully consider different definitions for the collective va...
We present the results of ab initio molecular dynamics (AIMD) simulations of the solution-air interface of aqueous lithium bromide (LiBr). We find that, in agreement with experimental data and previous simulation results with empirical polarizable force field models, Br⁻ anions prefer to accumulate just below the first molecular water layer near th...
We use non-equilibrium molecular dynamics simulations to study dipolar dumbbell fluids in a thermal gradient. We study the relative orientation of size asymmetric molecules with respect to the thermal gradient, and the sensitivity of the orientation to whether the Wolf method or Ewald summation is employed to compute the electrostatic interactions....
We investigate, using non-equilibrium molecular dynamics simulations and theory, the response of molecular fluids confined in slit pores under the influence of a thermal gradient and/or an applied force. The applied force which has the same functional form as a gravitational force induces an inhomogeneous density in the confined fluid, which result...
Local electric field factors are calculated for liquid benzene by combining molecular dynamic simulations with a subsequent force-field model based on a combined charge-transfer and point-dipole interaction model for the local field factor. The local field factor is obtained as a linear response of the local field to an external electric field and...
Transport and dielectric properties of water and the influence of coarse-graining: Comparing BMW, SPC/E, and TIP3P models J. Chem. Phys. 140, 064107 (2014); 10.1063/1.4864117 Water polarization induced by thermal gradients: The extended simple point charge model (SPC/E) J. Chem. Phys. 139, 014504 (2013); 10.1063/1.4811291 How does water-nanotube in...
We use density functional theory to investigate the impact that strong electric fields have on the the structure and energetics of small lithium ion-water clusters, Li(+) • nH2O, with n=4, 6. We find that electric field strengths of ~0.5 V/Å are sufficient to break the symmetry of the n=4 tetrahedral energy minimum structure, which undergoes a tran...
We use molecular dynamics simulations in applied thermal gradients to study thermomolecular orientation (TMO) of size-asymmetric dipolar dumbbells with different molecular dipole moments. We find that the direction of the TMO is the same as in apolar dumbbells of the same size, i.e. the smaller atom in the dumbbell tends to orient towards the colde...
We study small clusters of water or methanol containing a single Ca(2+), Na(+), or Cl(-) ion with classical molecular dynamics simulations, using models that incorporate polarizability via the Drude oscillator framework. Evaporation and condensation of solvent from these clusters is examined in two systems, (1) for isolated clusters initially prepa...
We have developed a simple yet powerful method to allow the manipulation of liquid crystal molecules in molecular dynamics simulations with an orienting force. We describe this method and demonstrate its use with simulations of 2-(4-octyloxyphenyl)-5-octyloxypyrimidine to transform an isotropic initial configuration into either nematic or smectic c...
Aqueous nanoscale systems feature a distinct electrowetting behavior, sensitive to not only the strength but also the direction and polarity of the applied electric field. These effects have so far not been tested in solutions of ions, although electrolytes are commonly present in electrowetting experiments. We describe atomistic simulations of ses...
We apply molecular dynamics (MD) simulations to study the final phase of electrospray ionization (ESI), where an ion loses all of its associated solvent molecules. By applying an electric field to a cluster of H(2)O molecules solvating an ion and including a surrounding gas of varying pressure, we demonstrate that collisions with the gas play a maj...
Applying an electric field is a well-established experimental method to tune surface wettability. As accessible experimental length scales become shorter, the modification of interfacial properties of water using electric field must come to grips with novel effects existing at the nanoscale. We survey recent progress in understanding these effects...
To understand the role of interfacial water on nanostructred surfaces is important for materials science and biology. The talk will describe some of our recent progress in predicting and understanding the effects of nanopatterning on topologically or chemically heterogeneous surfaces on wetting via in silico experiments.
We examine the effect of nanoscale roughness on spreading and surface mobility of water nanodroplets. Using molecular dynamics, we consider model surfaces with sub-nanoscale asperities at varied surface coverage and with different distribution patterns. We test materials that are hydrophobic, and those that are hydrophilic in the absence of surface...
We study the effect of electric field on interfacial tension of nanoconfined water [1,2] using molecular simulations. Our analysis and simulations confirm that classical electrostriction characterizes usual electrowetting behavior in nanoscale hydrophobic channels and nanoporous materials [3]. We suggest a new mechanism to orient nanoparticles by a...
We use atomistic simulations to study the orientational dynamics of a nonpolar nanoparticle suspended in water and subject to an electric field. Because of the molecular-level effects we describe, the torque exerted on the nanoparticle exceeds continuum-electrostatics-based estimates by about a factor of 2. The reorientation time of a 16.2 x 16.2 x...
We studied monosodium glutamate (MSG) in aqueous solution using molecular dynamics simulations and compared the results with recent neutron diffraction with isotope contrast variation/empirical potential structure refinement (EPSR) data obtained on the same system (McLain et al. J. Phys. Chem. B 2006, 110, 21251-21258). We used classical simulation...
Interfacial polar molecules feature a strongly anisotropic response to applied electric field, favoring dipole orientations parallel to the interface. In water, in particular, this effect combines with generic orientational preferences induced by spatial asymmetry of water hydrogen bonding under confined geometry, which may give rise to a Janus int...
We study the behavior of ambient temperature water under the combined effects of nanoscale confinement and applied electric field. Using molecular simulations we analyze the thermodynamic causes of field-induced expansion at some conditions, and contraction at others. Repulsion among parallel water dipoles and mild weakening of interactions between...
We study the behavior of ambient temperature water under the combined effects of nanoscale confinement and applied electric field. Using molecular simulations we analyze the thermodynamic causes of field-induced expansion at some, and contraction at other conditions. Repulsion among parallel water dipoles and mild weakening of interactions between...
We manifest a significant influence of field direction and polarity on surface wetting, when the latter is tuned by application of an external electric field. Thermodynamics of field-induced filling of hydrocarbon-like nanopores with water is studied by open ensemble molecular simulation. Increased field strength consistently results in water-filli...
Using molecular simulations of nanosized aqueous droplets on a model graphite surface, we demonstrate remarkable sensitivity of water contact angles to the applied electric field polarity and direction relative to the liquid/solid interface. The effect is explained by analyzing the influence of the field on interfacial hydrogen bonding in the nanod...
The adsorption of CO2 gas on the MgO (100) crystal surface is investigated using grand canonical Monte Carlo simulations. This allows us to obtain adsorption isotherms that can be compared with experiment, as well as to explore the possible formation of monolayers of different densities. Our model calculations agree reasonably well with the availab...
The liquid/vapor criticality of Coulombic and other fluids characterized by longrange interactions is investigated using canonical
and grand-canonical Monte Carlo computer simulations. It is shown that while mixed-field finite-size scaling methods appear
consistent with the theoretically expected universality class (Ising or classical depending on...
We consider a near-critical fluid of hard spheres with short-range interactions (approximately r(-6)) and obtain its constant-volume heat capacity C(V) by means of Monte Carlo calculations in the canonical ensemble. The question addressed is whether or not the heat capacities of the finite-size systems studied in simulations can provide a reliable...
The vapor–liquid criticality of a fluid of charged hard dumbbells is investigated employing grand canonical Monte Carlo simulations and mixed-field finite-size scaling methods. The reduced critical temperature and density obtained are T c *0.049110.00003 and c *0.1010.003, respectively. The critical temperature is very close to that of the restrict...
The constant-volume heat capacities, C V , of various near-critical fluids with long-range potentials have been obtained using both canonical and grand-canonical Monte Carlo GCMC calculations. In the case of the restricted primitive model it is shown that the large discrepancies between previously reported results arise from the use of different si...
Two studies of aspects of modelling dipole moment functions of XH bonds in small molecules for use in calculating overtone intensities have been undertaken. The first study deals with the fitting of ab initio calculations of the dipole moment at discrete points to a functional form. The two methods that are compared are the use of least-squares reg...
Two studies of aspects of modelling dipole moment functions of XH bonds in small molecules for use in calculating overtone intensities have been undertaken. The first study deals with the fitting of ab initio calculations of the dipole moment at discrete points to a functional form. The two methods that are compared are the use of least-squares reg...
XH-stretching vibrational band intensities have been calculated for seven small molecules with OH, NH and CH bonds, respectively, using the simple harmonically coupled anharmonic oscillator local mode model and ab initio dipole moment functions, both expressed in XH-stretching bond coordinates. The dipole moment functions were calculated with a tri...
As accessible experimental length scales become shorter, the modification of interfacial properties of water using electric field (electrowetting) must come to grips with novel effects existing at the nanoscale. I will briefly survey some of our recent progress we have made in understanding these effects using molecular simulations.
Molecular simulations of nanosized aqueous droplets and films next to apolar surfaces show a remarkable sensitivity of water contact angles on the applied electric field polarity and direction relative to the liquid/solid interface. We explain the effect by analyzing the influence of the field on interfacial hydrogen bonding which in turn affects t...
Questions
Question (1)
I just attended a talk on new photovoltaics, and it reminded me of a question I've had before. All of these systems generate a lot of waste heat. Shouldn't there be a smart way to couple these systems to some sort of heat engine and get some added power generation that way? Seems this should be easier than spending millions of dollars to get another 5% in electrical conversion efficiency. I can't be the first one to think of this, so any suggestions for further reading would be appreciated.
