Polystyrene Penetrates Lipid Vesicles

Side by Side View
Full view
Inner View

This video demonstrates a molecular dynamics simulation of a polystyrene nanoplastic particle penetrating a lipid vesicle. Two different viewpoints are included: Left: PS with both outer and inner leaflets visualized. Right: PS with only the inner leaflet visualized. PS is included in gray, inner leaflet in cyan, and outer leaflet in red.

Key things to note:

– PS penetrates quickly (video timescale is total of 1.2 microseconds)

– Inner leaflet remains relatively intact over the course of the video

This is part of work funded by the National Science Foundation as a part of the Center for Sustainable Nanotechnology. https://susnano.wisc.edu/

This has been added as a virtual component of a poster presentation.

Towards an Understanding of the Activation Energies in Liquid Water

My research is focused on how the dynamical and structural prop- erties of liquids change with temperature (T) and pressure (p). Specifically, I have developed methods for calculating the derivatives of dynamical timescales with respect to T and p from molecular dynamics simulations at a single temperature and pressure.[1−8] This method provides previously unobtainable mechanistic insight via decomposition of activation energies into contributions from molecular interactions. My work has enhanced our understanding of diffusion,[1-2] reorientation,[1,3,7] viscosity,[5] and hydrogen bond exchanges[8] in liquid water, while also revealing more about the nature of activation energies.

tdep.png
Figure 1: Prediction of the water diffusion coefficient from room tem- perature simulations (blue) compared to results from simulations at different temperatures (black) and exper- imental measurements[10] (red). Reprinted with permission from Piskulich, Z.A. & Thompson, W.H. J. Chem. Phys., 152, 074505 (2020). Copyright 2020, AIP Publishing.
A feature of this method is that it determines the analytical derivatives at a particular T and p rather than being calculated numerically using a range of temperatures and pressures as is done in an Arrhenius analysis. This allows activation energies to be extracted even for dynamical timescales that are non-Arrhenius (e.g., liquid water diffusion), or where the temperature ranges needed for an Arrhenius analysis are not accessible (e.g., near a phase transition).

 

We have illustrated how derivatives of the diffusion coefficient, reorientation times, and liquid structure may be used to predict the temperature dependence of these quantities deeply into the supercooled regime. For example, from room temperature simulations we used our method to predict the diffusion coefficient of water down to 125 K and found it to be in agreement with experimental measurements,[9] as shown in Figure 1.[7]

A century ago Tolman showed that the activation energy can be understood as the excess energy needed to surmount the barrier (as opposed to the common view of the height of the barrier).[10] The activation energy decompositions obtained from our method, then provide an accounting of the excess energy of a particular type (electrostatic, kinetic, etc.) required to surmount such a barrier. In every dynamical process in water that we have studied, we have found that the the Lennard-Jones and electrostatic activation energy contributions are in competition with one another, with the latter dominating. This is consistent with the energetic changes involved in breaking a hydrogen bond, as illustrated schematically in Figure 2.[8]

 

Picture2.png
Figure 2: Comparison of TIP4P/2005 activation en- ergy decompositions for diffusion, reorientation, viscosity, and hydrogen bond exchanges in liquid water.

We are developing this work in a number of directions, including ongoing collaborations with Chris Mundy, Greg Schenter, Damien Laage, and Elise Diboué-Dijon. In the future, this method should allow insight into activation energies in other cases where an Arrhenius analysis is difficult, for instance a system at phase coexistence. We are also extending the decompositions to the level of individual molecular interactions (e.g., the effect of particular residues on the reorientation activation energy of a water molecule in a protein hydration shell).

References: [1] Piskulich, Z. A., Mesele, O. O. & Thompson, W. H. J. Chem. Phys. 147, 134103 (2017). [2] Piskulich, Z. A., Mesele, O. O. & Thompson, W. H. J. Chem. Phys. 148, 134105 (2018). [3] Piskulich, Z. A. & Thompson, W. H., J. Chem. Phys. 149, 164504 (2018). [4] Piskulich, Z. A., Mesele, O. O., & Thompson, W. H. J. Phys. Chem. A. 123, 7185-7194 (2019). [5] Mendis, C. H., Piskulich, Z. A. & Thompson, W. H. J. Phys. Chem. B. 123, 5857-5865 (2019). [6] Piskulich, Z.A. & Thompson, W.H. J. Chem. Phys. Commun., 152, 011102 (2020). [7] Piskulich, Z.A. & Thompson, W.H. J. Chem. Phys., 152, 074505 (2020). [8] Piskulich, Z.A., Laage, D., & Thompson, W.H. J. Chem. Phys. submitted (2020). [9] Xu, Y., Petrik, N.G., Smith, R.S., Kay, B.D. & Kimmel, G.A. Proc. Natl. Acad. Sci. 113, 14921 (2016). [10] Tolman, R. C. J. Am. Chem. Soc. 42, 2506–2528 (1920).

NSF GRFP Annual Report: Year 2

During my second year of support from the NSF Graduate Research Fellowship Program (GRFP) I have made strides in my academic progress, my professional development, and my research. I should note, I also took my NSF GROW trip this year to Paris to work with Damien Laage; however, the COVID-19 crisis occurred within the first two weeks of this experience. 

My research focuses on developing new simulation and analysis techniques for understanding how molecular motions influence chemical reactions (e.g., catalysis). Throughout my time on the NSF fellowship I have been developing techniques for understanding the temperature dependence of these motions, as well as that of molecular structure. The developed technique allows not only for the calculation of activation energies, which control the temperature dependence of these quantities, but also the temperature dependence of these activation energies. With this information we have shown that it is possible to use it to predict the motions and structures of complex liquids (e.g. water) over large temperature ranges. Additionally, the developed methods provide mechanistic insight, unavailable by any other method, into how these motions and structures originate from specific molecular interactions.

Intellectual Merit: There however remains a scientific debate about the specific structures and motions that water undergoes when supercooled, and whether these are apparent at room temperature. In our work over the past year, we have developed the above techniques for predicting the temperature dependence of both molecular motions (diffusion,reorientation) as well as liquid structure in order to help resolve this debate. Thus far, we have shown that the motions of water can be predicted over wide range of temperatures reaching deeply into the supercooled regime (down to 125 K in some cases, about 150 K below the freezing point) from room temperature. We have similarly shown that the structure supercooled water can be predicted down to 235 K from room temperature, and are currently developing techniques for predicting even lower temperatures. Taken together, this indicates that the strange behavior observed and debated over in the scientific literature must have origins that are present in the intermolecular interactions present at room temperature.

Broader Impacts: It has been estimated that most of the water in the universe exists as a supercooled liquid, or a liquid that has been cooled slowly enough that it remains liquid-like instead of freezing at temperatures well below its freezing point. Indeed on earth, certain species of insects have developed specific proteins that suppress freezing in water to remain viable in extreme environments. By better understanding supercooled water, we can better understand these processes as well.

Over the past year, I have participated in multiple professional development experiences and scientific conferences. As the vice-president of the Chemistry graduate student organization at KU I helped develop a weekly professional development seminar series, as well as an Alumni careers panel. I also helped organize the The Physics and Chemistry of Liquids Gordon Research Seminar which was held in Holderness, New Hampshire, August 2019. I attended both the aforementioned conference along with the associated Gordon Research Conference as well as the Pacific Conference on Spectroscopy and Dynamics, where I presented a contributed talk on my research. The research presented at that conference was also included in a Viewpoint article in the Journal of Physical Chemistry. During my time, I have also been involved in mentoring two other graduate students as well as two undergraduate students.

Why it matters: “On the temperature dependence of liquid structure”

In our recent paper, “On the temperature dependence of liquid structure” published here, we present a method for calculating temperature derivatives of the radial distribution function from a simulation at a single temperature.

Wait, what do you mean liquid structure?

When we think of liquids – structure might be the last thing on your mind. After all, when you pour water into a cup, it immediately conforms to the shape of the cup. When we say liquid structure, we mean that when you look on the molecular level at any given molecule, it has interactions with the molecules around it. On average, this make it so there are certain distances at which other molecules are more likely to be found and similarly other distances at which other molecules are less likely to be found around our chosen molecule when compared to molecules that are too far away to feel these interactions (they instead feel a much stronger influence from molecules that are close to them). The radial distribution function (RDF), is a mathematical tool used by scientists to describe this ordering by counting the molecules found at a given distance away from the chosen molecule and then comparing whether at that distance the count is larger than what would be expected if the chosen molecule was not present (more ordered) or smaller (less ordered).

RDF.png

As we walk outwards from our chosen molecule, the RDF first has a region where no molecules are present (the above plot is zero). This occurs because our chosen molecule takes up space so no other molecules can be found there! Then we find a very large peak to the right of this region that indicating a region where molecules are more likely to be found surrounding our molecule, this is typically referred to as the first solvation shell. This is quickly followed by a region of depletion as the molecules in that first solvation shell all also take up space. These molecules all also cause ordering around themselves as well, causing a new region of greater order after that depletion, called the second solvation shell. The further out we move this alternating pattern of peaks and depletions gets weaker as less of the ordering is caused by our particular chosen molecule. Eventually, at very long distances there is no ordering from our chosen molecule and the RDF goes to a value of 1 (random ordering).

Okay, but why do we care?

For computational chemists, like myself, one of the first analysis most of us write are codes to calculate the RDF. A number of properties and molecular processes are directly related to the structure of the liquid. For instance, the process by which molecules move in a liquid, called diffusion, can be thought of as moving between the first and second solvation shells. The depth of the depletion between these solvation shells is related to  (by a mathematical expression that I won’t delve into here) the ease at which molecules are able to diffuse within a particular liquid. A very crude way of thinking about this is in terms of two liquids, one viscous e.g. molasses, and one not e.g. water. The viscous one might have a deeper depletion in the RDF than the non-viscous one, making it more difficult for molecules to diffuse in molasses than in water. This is an imprecise way of describing this; however, this is just one of many ways that scientists can use the RDF to their advantage.

What I have yet to mention; however, is the importance of temperature as it relates to the RDF. As the temperature of a liquid changes, so does its structure. For instance, if you cool liquid water the peaks and depletions become significantly larger. In terms of the discussion of the previous paragraph, this means that things like diffusion also become more difficult as temperature is lowered. One key part of our work is that we have developed a way of predicting how temperature changes the RDF using only the information available from a single room temperature. In the video below, you can see how the predictions (red line) from room temperature (298 K) work over a large range of temperatures from predicting down to 235 K (blue line) up to 360 K (purple line).

In our work, we show that this method works very well for liquid water and can give us new scientific tools for understanding how its structure changes with temperature.

 

NSF GRFP Annual Report: Year 1

As a part of the NSF Graduate Research Fellowship Program I am expected to prepare a report on my activities over the last year. It is supposed to be accessible to the public. So here is year one:

During my first year of support from the NSF Graduate Research Fellowship Program (GRFP) I have made strides in my academic progress, my professional development, and my research.

My research focuses on developing new simulation and analysis techniques for understanding how molecular motions influences chemical reactions (e.g., catalysis). Frequently, molecular motions, such as diffusion and reorientation, are calculated from molecular dynamics simulations. In my work, I have focused on the development of new approaches that can describe the temperature and pressure dependence of these motions. These new methods allow for the calculation of activation energies, which are frequently calculated as a measure of how these processes change with temperature. The developed methods provide mechanistic insight, unavailable by any other method, into these processes through the decomposition of these activation energies into contributions from specific molecular interactions.

Intellectual Merit: In the past year we have used these methods to identify and examine the root cause of differences in activation energies of water reorientation measured by two experimental techniques, pump-probe IR and NMR spectroscopy. Activation energies measured by NMR include not only the temperature dependence of the reorientation timescales measured by pump-probe experiments, but an additional factor due to the changing amplitude of these timescales with temperature. Additionally, we have developed a formalism by which our developed TCFs may be used to make predictions of the reorientation time over a large temperature range from simulations at a single temperature. I have also worked on an extension of this method with another graduate student to calculate the decomposition of the shear viscosity activation energies. A fourth project is the extension of this method to ab initio MD simulations of lithium fluoride ion pairing in collaboration with Drs. Chris Mundy and Greg Schenter at Pacific Northwest National Laboratory (PNNL). As a part of this project I traveled to PNNL to implement support these state-of-the-art simulations into my code. Lastly, I have been calculating the mobility of lithium perchlorate ions in carbon dioxide-expanded acetonitrile in order to understand the effect of CO2-expansion on ion mobilities to enhance our understanding of electrochemical experiments in these complex reaction media.

Broader Impacts: I have participated in a number of professional development activities as well as service in the scientific community. In 2018 I was elected president of the KU Chemistry Graduate Student Organization (ChemGSO), and I have continued on in 2019 as the Vice-President. During my time working with ChemGSO I helped it gain student organization status, increased graduate student involvement on departmental committees, found new avenues for fundraising for our organization, and assisted ChemGSO, the College of Graduate Affairs, and various other STEM GSOs in implementing a weekly professional development series, called ASCEND. I have also participated for the last year as a co-chair of the 2019 Gordon Research Seminar on the Physics and Chemistry of Liquids which will meet in July. In the past year I have given a number of poster presentations, including the 2018 Water Gordon Research Conference, the 2019 Kansas Physical Chemistry Symposium, and the 2019 Pacific Conference on Spectroscopy and Dynamics.

Building a Better Graduate Student Organization

Talking to other graduate students and professors at conferences over the last couple years I have realized that for the most part, STEM graduate student organizations (GSOs) typically focus on one (or more) of the following:

  1. Social Activities: These activities exist primarily to develop social ties between members and their departments.
  2. Advocacy:  This includes participation on departmental/university committees, pushes for graduate student interests, and community outreach.
  3. Professional Development: This includes development of new professional development and networking opportunities. Additionally, existing opportunities are actively sought out.

As an example, when I first got to the University of Kansas, our GSO was primarily run by 1-2 people and existed solely to plan the recruiting weekend, welcome picnic, and halloween party. This placed our GSO heavily on the Social side of the scale. Lately, our GSO has shifted towards trying to do all three (though we are still weighted heavily towards social).

What I have learned from my discussions with others is that most GSOs do not cover all areas described above; however, with some (relatively) simple changes, your GSO can start to grow in these areas and become something greater.

1. Build a Leadership Team

Many GSOs which are struggling to do a variety of activities, struggle because every activity requires the attention of the 1-2 people in charge of the organization. If you have a devoted group of ~5 people who are willing to take charge of planning events, you can spread out the responsibilities among them. This also helps reduce event-planning burnout, while allowing your organization to tackle more.

When developing your leadership team you need to take a few things into account. STEM departments are widely varied and your leadership team should reflect that. Ideally, each major division in your department should have representation on your team. This allows your leadership team to split the effort in advertising your events to your department, and increases the draw to the events that you plan. If you can’t get someone from certain divisions at first – don’t fear! – as your GSO grows, interest in serving on your GSO leadership team will grow.

Your team should also span multiple generations of graduate students in your department. Ideally, you will find a number of devoted students early in their graduate careers that will take ownership of your organization. Participation of younger students also reduces the likelihood that your organization will die out when members of your team graduate. Ideally, every year there should be new younger students that cycle into your GSO as older students graduate or step back. Additionally, reaching out to a trusted faculty member to act as an advisor to your organization can play a key role in building up your presence within your department.

2. Determine your Vision

Start off by determining what you want from your GSO. Many graduate students get caught without an overall vision for the change they want to be in their department. Additionally, many GSOs underestimate the amount of support they can obtain from their department to pull off larger-scale events (as our department reminds us repeatedly, if we succeed they do too!). I’ve included some sample questions for you to bring to your GSO to start get the ball rolling on thinking about a vision — you should discuss these and write these down with your leadership team.

general questions

  1. What is your current fundraising plan? Do you have goals for how much you want to raise over the next year?
  2. Do you have a budget? (You should have at least a rough budget!)
  3. If money wasn’t an object, what event would you want to try to create for your program.
  4. Who are the administrators in your program who exist solely to benefit graduate students?

social activities questions

  1. How many social activities are there for graduate students to bond with one another?
  2. How effective are these social activities? Do they cover the same people every time – or do they encourage mixing between groups and divisions?
  3. Are there some social activities that are not centered around alcohol?
  4. How frequently does your organization want to plan a social event? How much of your money are you going to put towards these?

advocacy questions

  1. Are their any glaring issues in your program? Is there a lack of safety/ethics training? Is morale low among graduate students?
  2. Do graduate students have a voice in your department?
  3. If you could change something about how your program works, what would you change?
  4. How open are lines of communication between students, faculty, and the department?
  5. When graduate students have a concern about something – who do they go to?

professional development questions

  1. What is the attitude in your department towards professional development? Is there a high focus on it already from other sources? Are students going out of their way to find prof-dev events to participate in?
  2. What are recent, successful, professional development activities that have taken place in your department?
  3. Do you notice any holes in the current programming? Are all of the activities centered on careers in academia when many graduate students want to go into industry?
  4. How involved are current graduate students with alumni? Are alumni coming back and talking about their career experiences? Is there a means by which graduate students can reach out to alumni for help networking/job-finding?
  5. Are there centers on campus that put on professional development events for STEM students? Could you bring them into your department to help run things.

3. Solicit Feedback

Okay – so you have a leadership team and you have a vision. Now is a good time to touch base outside of your leadership team. I recommend drafting a constitution for your GSO (most universities require this for student org status anyway!)  You can find ours here. A constitution not only makes you write down many of your answers in Section 2 in an organized manner – but also it makes you organize them and think about how they fit into your organization. Think of a constitution as your framework plan of what you want your organization to become (not necessarily what it currently is). Your constitution should clearly reflect your mission, your goals, and what you are as an organization.

Sample constitution sections:

I. Name and Purpose (Vision!)

II. Membership

III. Officers

IV. Fundraising

V. Meetings

VI. Committees

VII. Events

VIII. Amendments

When you have your constitution – introduce your organization to graduate students and send your constitution out asking for feedback. Once you get it – discuss it with your leadership team, incorporate it, and then send the constitution out for a vote of graduate students. It is important to include all students in your department in this process, as the more involved they are the more pull they will feel to attend/volunteer in your GSO later.

After passing your constitution, it is important to continue solicit feedback. Plan monthly (or more frequently!) meetings of your GSO that are open to graduate students, where they can offer ideas or help with current projects. Keep in touch via email, letting them know what you have been working on lately. Start a Facebook/LinkedIN group where graduate students can connect with your organization and hear about upcoming events.

4. Be Inclusive and Transparent

A common mistake made by graduate student organizations is that they act too much in the shadows. If you plan something – take credit for it! Your goal should be to reach out to students in your department at least once a month (or even more if you started a Facebook/LinkedIN group). The more open you are about what you’re doing, the more likely that graduate students will see how they could fit into your organization.

On that note, you need to be inclusive to ideas that don’t originate from your leadership team. If someone comes to you with an event idea that they are really excited about, ask them what help they need to implement it. Give them ownership of their idea, and assist them in making it a reality. If your GSO actively hears ideas and implements them, that encourages more ideas from graduate students. If you get a reputation of being a black hole where ideas die, then you will get less participation. Additionally, the more that graduate students outside of your leadership team are involved in your organization, the less strain there is on your team. Ideally, your team will eventually move to a more advisory role helping to organize the overall efforts of graduate students in the department.

5. Don’t be Discouraged

Building a GSO takes time and effort. When you are first starting out, your monthly meetings might only be your leadership team. As you begin to do more your department will start to notice, and more students will want to be involved. Having the discussions mentioned earlier in this post are the first steps into building a self-sustaining GSO – but only with TLC and patience will your GSO grow.

Look out for my upcoming posts that will go into greater detail on how to develop the social activities, advocacy, and professional development aspects of your GSO.

Have anything to add? Feel free to leave a comment below!

Prename: A Better Rename

In this tutorial, I quickly run through how to get a better version of the rename utility in perl and use it to rename a series of files that have the same string that needs to be replaced.

The Problem:

I have a set of three files that need to have their names changed from having an “f” in them to a “br”. These files are:

f_dang.connect
f_dang.names
f_dang.paircoeffs

The Trivial Solution:

Obviously, with three files three simple mv commands would suffice; however, I was wondering what I would do if I needed to rename 100 files.

The Slightly-Less (But Still Pretty) Trivial Solution:

This is where I fell into the proverbial rabbit hole. On our HPC system we only had the regular linux rename utility, which is great when you have files named foo1, foo2, and foo3 and you need to make them foo001, foo002, and foo003 — but not great for a situation such as ours.

That is where prename comes in: prename is the perl version of the rename utility. It allows for a sed-like find replace interface for filenames. Better yet, it is possible to use the script without needing superuser access.

I downloaded the perl script (available as a gist here:). As a gist, this is available via a simple clone command.

Then, set your path environment variable to include the folder where you downloaded the perl script to. I made a folder called “prename”. This can be done by adding the following to your bashrc,

export PATH="~/prename:$PATH"

Once this is done, give the perl script execute permissions.

chmod +x prename.pl

Then you are good to go! Renaming is as simple as:

prename.pl 's/f_/br_/g' *