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Nils E. R. Zimmermann

Nils (Nisse) E. R. Zimmermann
Postdoctoral Fellow
Computational Science
Phone: (510)-486-7749
Fax: (510)-486-5812
Lawrence Berkeley National Laboratory
1 Cyclotron Road
MMS 50F-1650
Berkeley, CA 94720 US


I am a computational researcher active at the interface between physical chemistry and materials science.

My background and interests comprise adsorption and diffusion in porous media, nucleation and polymorph selection, as well as defects in materials.  The methods that I usually apply are classical simulations such as Monte Carlo and molecular dynamics based on interatomic potentials.  Because the phenomena on which I focus are often exceptionally slow, I frequently combine the classical simulations with rare-event methods to circumvent the time-scale problem.

At Berkeley Lab, I am expanding my methodological background by using Kohn-Sham density functional theory to calculate defect-formation energies and solid-state diffusion rates.  Since I am part of the Materials Project, my work aims at performing those calculations maximally automated to allow for a high-throughput data generation.

Should you be interested in any collaboration with me, just drop me an email.  I will be very happy to respond to you as soon as possible.

Thank you for your time and interest in my research,


Journal Articles

Nils E. R. Zimmermann, Maciej Haranczyk, "History and Utility of Zeolite Framework-Type Discovery from a Data-Science Perspective", Crystal Growth & Design, May 2, 2016,

Mature applications such as fluid catalytic cracking and hydrocracking rely critically on early zeolite structures. With a data-driven approach, we find that the discovery of exceptional zeolite framework types around the new millennium was spurred by exciting new utilization routes. The promising processes have yet not been successfully implemented (“valley of death” effect), mainly because of the lack of thermal stability of the crystals. This foreshadows limited deployability of recent zeolite discoveries that were achieved by novel crystal synthesis routes.

Watch a movie illustrating our seeded simulation strategy here.

Tobias Titze, Alexander Lauerer, Lars Heinke, Christian Chmelik, Nils E. R. Zimmermann, Frerich J. Keil, Douglas M. Ruthven, Jörg Kärger, "Transport in Nanoporous Materials Including MOFs: The Applicability of Fick’s Laws", Angew. Chem. Int. Ed., 2015, doi: 10.1002/anie.201506954

Diffusion in nanoporous host–guest systems is often considered to be too complicated to comply with such “simple” relationships as Fick’s first and second law of diffusion. However, it is shown herein that the microscopic techniques of diffusion measurement, notably the pulsed field gradient (PFG) technique of NMR spectroscopy and microimaging by interference microscopy (IFM) and IR microscopy (IRM), provide direct experimental evidence of the applicability of Fick’s laws to such systems. This remains true in many situations, even when the detailed mechanism is complex. The limitations of the diffusion model are also discussed with reference to the extensive literature on this subject.


Nils E. R. Zimmermann, Bart Vorselaars, David Quigley, Baron Peters, "Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates", J. Am. Chem. Soc., 2015, doi: 10.1021/jacs.5b08098

Nucleation and crystal growth are important in material synthesis, climate modeling, biomineralization, and pharmaceutical formulation. Despite tremendous efforts, the mechanisms and kinetics of nucleation remain elusive to both theory and experiment. Here we investigate sodium chloride (NaCl) nucleation from supersaturated brines using seeded atomistic simulations, polymorph-specific order parameters, and elements of classical nucleation theory. We find that NaCl nucleates via the common rock salt structure. Ion desolvation—not diffusion—is identified as the limiting resistance to attachment. Two different analyses give approximately consistent attachment kinetics: diffusion along the nucleus size coordinate and reaction-diffusion analysis of approach-to-coexistence simulation data from Aragones et al. (J. Chem. Phys. 2012, 136, 244508). Our simulations were performed at realistic supersaturations to enable the first direct comparison to experimental nucleation rates for this system. The computed and measured rates converge to a common upper limit at extremely high supersaturation. However, our rate predictions are between 15 and 30 orders of magnitude too fast. We comment on possible origins of the large discrepancy.

Watch a movie illustrating our seeded simulation strategy here.

Nils E. R. Zimmermann, Timm J. Zabel, Frerich J. Keil, "Transport into Nanosheets: Diffusion Equations Put to Test", J. Phys. Chem. C, 2013, 117:7384-7390, doi: 10.1021/jp400152q

Ultrathin porous materials, such as zeolite nanosheets, are prominent candidates for performing catalysis, drug supply, and separation processes in a highly efficient manner due to exceptionally short transport paths. Predictive design of such processes requires the application of diffusion equations that were derived for macroscopic, homogeneous surroundings to nanoscale, nanostructured host systems. Therefore, we tested different analytical solutions of Fick’s diffusion equations for their applicability to methane transport into two different zeolite nanosheets (AFI, LTA) under instationary conditions. Transient molecular dynamics simulations provided hereby concentration profiles and uptake curves to which the different solutions were fitted. Two central conclusions were deduced by comparing the fitted transport coefficients. First, the transport can be described correctly only if concentration profiles are used and the transport through the solid–gas interface is explicitly accounted for by the surface permeability. Second and most importantly, we have unraveled a size limitation to applying the diffusion equations to nanoscale objects. This is because transport-diffusion coefficients, DT, and surface permeabilities, α, of methane in AFI become dependent on nanosheet thickness. Deviations can amount to factors of 2.9 and 1.4 for DT and α, respectively, when, in the worst case, results from the thinnest AFI nanosheet are compared with data from the thickest sheet. We present a molecular explanation of the size limitation that is based on memory effects of entering molecules and therefore only observable for smooth pores such as AFI and carbon nanotubes. Hence, our work provides important tools to accurately predict and intuitively understand transport of guest molecules into porous host structures, a fact that will become the more valuable the more tiny nanotechnological objects get.

Watch a movie illustrating the transient molecular dynamics approach, which was critical for this study, here.

Nils E. R. Zimmermann, Berend Smit, Frerich J. Keil, "Predicting Local Transport Coefficients at Solid-Gas Interfaces", J. Phys. Chem. C, 2012, 116:18878-1888, doi: 10.1021/jp3059855

The regular nanoporous structure make zeolite membranes attractive candidates for separating molecules on the basis of differences in transport rates (diffusion). Since improvements in synthesis have led to membranes as thin as several hundred nanometers by now, the slow transport in the boundary layer separating bulk gas and core of the nanoporous membrane is becoming increasingly important. Therefore, we investigate the predictability of the coefficient quantifying this local process, the surface permeability α, by means of a two-scale simulation approach. Methane tracer-release from the one-dimensional nanopores of an AFI-type zeolite is employed. Besides a pitfall in determining α on the basis of tracer exchange, we, importantly, present an accurate prediction of the surface permeability using readily available information from molecular simulations. Moreover, we show that the prediction is strongly influenced by the degree of detail with which the boundary region is modeled. It turns out that not accounting for the fact that molecules aiming to escape the host structure must indeed overcome two boundary regions yields too large a permeability by a factor of 1.7–3.3, depending on the temperature. Finally, our results have far-reaching implications for the design of future membrane applications.

Watch a movie illustrating the conditions of self- or tracer-diffusion here.

Nils E. R. Zimmermann, Sayee P. Balaji, Frerich J. Keil, "Surface Barriers of Hydrocarbon Transport Triggered by Ideal Zeolite Structures", J. Phys. Chem. C, 2012, 116:3677-3683, doi: 10.1021/jp2112389

Shedding light on the nature of surface barriers of nanoporous materials, molecular simulations (Monte Carlo, Reactive Flux) have been employed to investigate the tracer-exchange characteristics of hydrocarbons in defect-free single-crystal zeolite membranes. The concept of a critical membrane thickness as a quantitative measure of surface barriers is shown to be appropriate and advantageous. Nanopore smoothness, framework density, and thermodynamic state of the fluid phase have been identified as the most important influencing variables of surface barriers. Despite the ideal character of the adsorbent, our simulation results clearly support current experimental findings on MOF Zn(tbip) where a larger number of crystal defects caused exceptionally strong surface barriers. Most significantly, our study predicts that the ideal crystal structure without any such defects will already be a critical aspect of experimental analysis and process design in many cases of the upcoming class of extremely thin and highly oriented nanoporous membranes.

Watch here a movie that highlights how n-hexane molecules are adsorbed in a zeolite slab.

Nils E. R. Zimmermann, Maciej Haranczyk, Manju Sharma, Bei Liu, Berend Smit, Frerich J. Keil, "Adsorption and diffusion in zeolites: The pitfall of isotypic crystal structures", Mol. Simul., 2011, 37:986-989, doi: 10.1080/08927022.2011.562502

The influence of isotypic crystal structures on adsorption and diffusion of methane in all-silica LTA, SAS and ITE zeolites is studied. Results obtained with the experimental structures are compared with structure predictions and approximations that are commonly employed. The results indicate that diffusion coefficients are much more affected than Henry coefficients. In fact, orders of magnitude deviations in the diffusivity can be observed and a systematic parameter study finally gives rise to the correlation between structure sensitivity and diffusion-window size.

Nils E. R. Zimmermann, Berend Smit, Frerich J. Keil, "On the Effects of the External Surface on the Equilibrium Transport in Zeolite Crystals", J. Phys. Chem. C, 2009, 114:300-310, doi: 10.1021/jp904267a

With the aid of molecular simulation techniques (molecular dynamics, grand-canonical Monte Carlo, and reactive flux correlation function RFCF), the influence of the external surface on the equilibrium permeation of methane and ethane into and out of an AFI-type zeolite crystal has been studied. In particular, “extended dynamically corrected transition state theory”, which has been proven to describe the transport of tracers in periodic crystals correctly, has been applied to surface problems. The results suggest that the molecules follow paths that are close to the pore wall in the interior and also at the crystal surface. Moreover, the recrossing rate at the surface turns out to be non-negligible, yet, in contrast to the intracrystalline recrossing rate, remains almost constant over loading which gives indication to diffusive barrier crossing at the crystal surface. As a consequence of very different adsorption and desorption barriers, the corresponding permeabilities are shown to be not equal for one and the same condition (T and p). The critical crystal length, beyond which surface effects can be certainly neglected, is computed on basis of flux densities. Entrance/exit effects, in the present cases, are practically important solely for ethane at low pressures. The influence of the type of external surface on the surface flux is, hereby, rather small, because the transport at the surface is controlled by the slow supply from the gas phase. This has been evidenced by a simplified thermodynamic model that has been derived within this work and which is based on rapidly assessable simulation data. Finally, we propose a procedure for estimating the importance of different factors that have an impact on surface effects.

Baron Peters, Nils E. R. Zimmermann, Gregg T. Beckham, Jefferson W. Tester, Bernhardt L. Trout, "Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism", J. Am. Chem. Soc., 2008, 130:17342-1735, doi: 10.1021/ja802014m

Increased interest in natural gas hydrate formation and decomposition, coupled with experimental difficulties in diffusion measurements, makes estimating transport properties in hydrates an important technological challenge. This research uses an equilibrium path sampling method for free energy calculations [Radhakrishnan, R.; Schlick, T. J. Chem. Phys. 2004, 121, 2436] with reactive flux and kinetic Monte Carlo simulations to estimate the methane diffusivity within a structure I gas hydrate crystal. The calculations support a water-vacancy assisted diffusion mechanism where methane hops from an occupied “donor” cage to an adjacent “acceptor” cage. For pathways between cages that are separated by five-membered water rings, the free energy landscape has a high barrier with a shallow well at the top. For pathways between cages that are separated by six-membered water rings, the free energy calculations show a lower barrier with no stable intermediate. Reactive flux simulations confirm that many reactive trajectories become trapped in the shallow intermediate at the top of the barrier leading to a small transmission coefficient for these paths. Stable intermediate configurations are identified as doubly occupied off-pathway cages and methane occupying the position of a water vacancy. Rate constants are computed and used to simulate self-diffusion with a kinetic Monte Carlo algorithm. Self-diffusion rates were much slower than the Einstein estimate because of lattice connectivity and methane’s preference for large cages over small cages. Specifically, the fastest pathways for methane hopping are arranged in parallel (nonintersecting) channels, so methane must hop via a slow pathway to escape the channel. From a computational perspective, this paper demonstrates that equilibrium path sampling can compute free energies for a broader class of coordinates than umbrella sampling with molecular dynamics. From a technological perspective, this paper provides one estimate for an important transport property that has been difficult to measure. In a hydrate I crystal at 250 K with nearly all cages occupied by methane, we estimate D ≈ 7 × 10−15X m2/s where X is the fraction of unoccupied cages.

Nils E. R. Zimmermann, Sven Jakobtorweihen, Edith Beerdsen, Berend Smit, Frerich J. Keil, "In-Depth Study of the Influence of Host-Framework Flexibility on the Diffusion of Small Gas Molecules in One-Dimensional Zeolitic Pore Systems", J. Phys. Chem. C, 2007, 111:17370-1738, doi: 10.1021/jp0746446

Molecular-dynamics simulations are performed to understand the role of host−framework flexibility on the diffusion of methane molecules in the one-dimensional pores of AFI-, LTL-, and MTW-type zeolites. In particular, the impact of the choice of the host model is studied. Dynamically corrected Transition State Theory is used to provide insights into the diffusion mechanism on a molecular level. Free-energy barriers and dynamical correction factors can change significantly by introducing lattice flexibility. In order to understand the phenomenon of free-energy barriers reduction, we investigate the motion of the window atoms. The influence that host−framework flexibility exerts on gas diffusion in zeolites is, generally, a complex function of material, host model, and loading such that transferability of conclusions from one zeolite to the other is not guaranteed.